Sequences of hepatitis C virus genotypes and their use as therapeutic and diagnostic agents

ABSTRACT

The present invention relates to a polynucleic acid composition comprising or consisting of at least one polynucleic acid containing 8 or more contiguous nucleotides corresponding to a nucleotide sequence from the region spanning positions 417 to 957 of the Core/E1 region of HCV type 3; and/or the region spanning positions 4664 to 4730 of the NS3 region of HCV type 3; and/or the region spanning positions 4892 to 5292 of the NS3/4 region of HCV type 3; and/or the region spanning positions 8 023 to 8 235 of the NS5 region of the BR36 subgroup of HCV type 3a; and/or the coding region of HCV type 4a starting at nucleotide 379 in the core region; and/or the coding region of HCV type 4; and/or the coding region of HCV type 5, with said nucleotide numbering being with respect to the numbering of HCV nucleic acids as shown in Table 1, and with said polynucleic acids containing at least one nucleotide difference with known HCV type 1, and/or HCV type 2 genomes in the above-indicated regions, or the complement thereof.

This application is a continuation of application Ser. No. 08/362,455,filed Jan. 11, 1995, which is a 371 U.S. national phase ofPCT/EP94/01323, filed Apr. 27, 1994, which designated the U.S., theentire content of which is hereby incorporated by reference in thisapplication.

The present invention relates to new nucleotide and amino acid sequencescorresponding to the coding region of a new type 2 subtype 2d,type-specific sequences corresponding to HCV type 3a, to new sequencescorresponding to the coding region of a new subtype 3c, and to newsequences corresponding to the coding region of HCV type 4 and type 5subtype 5a; a process for preparing them, and their use for diagnosis,prophylaxis and therapy.

The technical problem underlying the present invention is to provide newtype-specific sequences of the Core, the E1, the F2, the NS3, the NS4and the NS5 regions of HCV type 4 and type 5, as well as of new variantsof HCV type 2 and 3. These new HCV sequences are useful to diagnose thepresence of type 2 and/or type 3 and/or type 4 and/or type 5 HCVgenotypes in a biological sample. Moreover, the availability of thesenew type-specific sequences can increase the overall sensitivity of HCVdetection and should also prove to be useful for therapeutic purposes.

Hepatitis C viruses (HCV) have been found to be the major cause ofnon-A, non-B hepatitis. The sequences of cDNA clones covering thecomplete genome of several prototype isolates have been determined (Katoet al., 1990; Choo et al., 1991; Okamoto et al., 1991; Okamoto et al.,1992). Comparison of these isolates shows that the variability innucleotide sequences can be used to distinguish at least 2 differentgenotypes, type 1 (HCV-J and HCV-1) and type 2 (HC-J6 and HC-J8), withan average homology of about 68%. Within each type, at least twosubtypes exist (e.g. represented by HCV-1 and HCV-J), having an averagehomology of about 79%. HCV genomes belonging to the same subtype showaverage homologies of more than 90% (Okamoto et al., 1992). However, thepartial nucleotide sequence of the NS5 region of the HCV-T isolatesshowed at most 67% homology with the previously published sequences,indicating the existence of a yet another HCV type (Mori et al., 1992).Pans of the 5′ untranslated region (UR), core, NS3, and NS5 regions ofthis type 3 have been published, further establishing the similarevolutionary distances between the 3 major genotypes and their subtypes(Chan et al., 1992).

The identification of type 3 genotypes in clinical samples can beachieved by means of PCR with type-specific primers for the NS5 region.However, the degree to which this will be successful is largelydependent on sequence variability and on the virus titer present in theserum. Therefore, routine PCR in the open reading frame, especially fortype 3 and the new type 4 and S described in the present inventionand/or group V (Cha et al., 1992) gels can be predicted to beunsuccessful. A new typing system (LiPA), based on v on in the highlyconserved 5′ UR, proved to be more usefull because the 5 major HCVgenotypes and their subtypes can be determined (Stuyver et al., 1993).The selection of high-titer isolates enables to obtain PCR fragments forcloning with only 2 primers, while nested PCR requires that 4 primersmatch the unknown sequences of the new type 3, 4 and 5 genotypes.

New sequences of the 5′ untranslated region (5′UR) have been listed byBukh et al. (1992). For some of these, the E1 region has recently beendescribed (Bukh et al., 1993). Isolates with similar sequences in the5′UR to a group of isolates including DK12 and HK10 described by Bukh etal. (1992) and E-b1 to E-b8 described and classified as type 3 by Chanet al. (1991), have been reported and described in the 5′UR, thecarboxyterminal part of E1, and in the NS5 region as group IV by Cha etal. (1992; WO 92/19743), and have also been described in the 5′UR forisolate BR56 and classified as type 3 by the inventors of tisapplication (Stuyver et al., 1993).

The aim of the present invention is to provide new HCV nucleotide andamino acid sequences enabling the detection of HCV infection.

Another aim of the present infection is to provide new nucleotide andamino acid HCV sequences enabling the classification of infectedbiological fluids into different serological groups unambiguously linkedto types and subtypes at the genome level.

Another aim of the present invention is to provide new nucleotide andamino acid HCV sequences ameliorating the overall HCV detection rate.

Another aim of the present invention is to provide new HCV sequences,useful for the design of HCV vaccine compositions.

Another aim of the present invention is to provide a pharmaceuticalcomposition consisting of antibodies raised against the polypeptidesencoded by these new HCV sequences, for therapy or diagnosis.

The present invention relates more particularly to a compositioncomprising or consisting of at least one polynucleic acid containing atleast 5, and preferably 8 or more contiguous nucleotides selected fromat least one of the following HCV sequences:

an HCV type 3 genomic sequence, more particularly in any of thefollowing regions:

the region spanning positions 417 to 957 of the Core/E1 region of HCVsubtype 3a,

the region spanning positions 4664 to 4730 of the NS3 region of HCV type3,

the region spading positions 4892 to 5292 of the NS3/4 region of HCVtype 3,

the region spanning positions 8023 to 8235 of the NS5 region of the BR36subgroup of HCV subtype 3a,

an HCV subtype 3c genomic sequence,

more particularly the coding regions of the above-specified regions;

an HCV subtype 2d genomic sequence, more particularly the coding regionof HCV subtype 2d;

an HCV type 4 genomic sequence, more particularly the coding region,more particularly the coding region of subtypes 4a, 4e, 4f, 4g, 4h, 4i,and 4j,

an HCV hype 5 genomic sequence, more particularly the coding region ofHCV type 5, more particularly the regions encoding Core, E1, E2, NS3,and NS4

with said nucleotide numbering being with respect to the numbering ofHCV nucleic acids as shown in Table 1, and with said polynucleic acidscontaining at least one nucleotide difference with known HCV (type 1,type 2, and type 3) polynucleic acid sequences in the above-indicatedregions, or the complement thereof.

It is to be noted that the nucleotide difference in the polynucleicacids of the invention may involve or not an amino acid difference inthe corresponding amino acid sequences coded by said polynucleic acids.

According to a preferred embodiment, the present invention relates to acomposition comprising or containing at least one polynucleic acidencoding an HCV polyprotein, with said polynucleic acid containing atleast 5, preferably at least 8 nucleotides corresponding to at leastpart of an HCV nucleotide sequence encoding an HCV polyprotein, and withsaid HCV polyprotein containing in its sequence at least one of thefollowing amino acid residues L7, Q43, M44, S60, R67, Q70, T71, A79,A87, N106, K115, A127, A190, V134, G142, I144, E152, A157, V158, P165,S177 or Y177, 1178, V180 or E180 or F182, R184, I186, H187, T189, A190,S191 or G191, Q192 or L192 or 1192 or V192 or E192, N193 or H193 orP193, W194 or Y194, H195, A197 or I197 or V197 or T197, V202, L103 orL203, Q208, A210, V212, F214, T216, R217 or D217 or E217 or V217, H218or N218, H219 or V219 or L219, L227 or I227, M231 or E231 or Q231, T232or D232 or A232 or K232, Q235 or I235, A237 or T237, I242, I246, S247,S248, V249, S250 or Y250, I251 or V251 or M251 or F251, D252, T254 orV254, L255 or V255, E256 or A256, M258 or F258 or V258, A260 or Q260 orS260, A261, T264 or Y264, M265, I266 or A266, A267, G268 or T268, F271or M271 or V271, I277, M280 or H280, 1284 or A284 or L84, V274, V291,N292 or S292, R293 or I293 or Y293, Q294 or R294, L297 or 1297 or Q297,A299 or Q299, N303 or T303, M308 or L308, T310 or F310 or A310 or D310or V310, L313, G317 or Q317, L333, S351, A358, A359, A363, S364, A366,T369, L373, F376, I387, S392, I399, F402, I1403, R40S, D454, A461, A463,T464, K484, Q500, E501, S521, K522, H524, N528, S531, S532, V534, F536,F537, M539, I546, C1282, A1283, H1310, V1312, Q1321, P1368, V1372,V1373, K1405, Q1406, S1409, A1424, A1429, C1435, S1436, S1456, H1496,A1504, D1510, D1529, I1543, N1567, D1556, N1567, M1572, Q1579, L1581,S1583, F1585, V1595, E1606 or T1606, M1611, V1612 or L1612, P1630,C1636, P1651, T1656 or I1656, L1663, V1667, V1677, A1681, H1685, E1687,G1689, V1695, A1700, Q1704, Y1705, A1713, A1714 or S1714, M1718, D1719,A1721 or T1721, R1722, A1723 or V1723, H1726 or G1726, E1730, V1732,F1735, I1736, S1737, R1738, T1739, G1740, Q1741, K1742, Q1743, A1744,T1745, L1746, E1747 or K1747, I1749, A1750, T1751 or A1751, V1753,N1755, K1756, A1757, P1758, A1759, H1762, T1763, Y1764, P2645, A2647,K2650, K2653 or L2653, S2664, N2673, F2680, K2681, L 2686, H2692, Q2695or L2695 or 12695, V2712, F2715, V2719 or Q2719, T2722, T2724, S2725,R2726, G2729, Y2735, H2739, I2748, G2746 or I2746, I2748, P2752 orK2752, P1754 or T2754, T2757 or P2157, with said notation being composedof a letter representing the amino acid residue by its one-letter code,and a number representing the amino acid numbering according to Kato etal., 1990.

Each of the above-mentioned residues can be found in any of FIGS. 2, 5,7, 11 or 12 showing the new amino acid sequences of the presentinvention aligned with known sequences of other types or subtypes of HCVfor the Core, E1, E2, NS3, NS4, and NS5 regions.

More particularly, a polynucleic acid contained in the compositionaccording to the present invention contains at least 5, preferably 8, ormore contiguous nucleotides corresponding to a sequence of contiguousnucleotides selected from at least one of HCV sequences encoding thefollowing new HCV amino acid sequences:

new sequences spanning amino acid positions 1 to 319 of the Core/E1region of HCV subtype 2d, type 3 (more particularly new sequences forsubtypes 3a and 3c), new type 4 subtypes (more particularly newsequences for subtypes 4a, 4e, 4f, 4g, 4h, 4i and 4j) and type 5a, asshown in FIG. 5;

new sequences spanning amino acid positions 328 to 546 of the E1/E2region of HCV subtype 5a as shown in FIG. 12;

new sequences spanning amino acid positions 1556 to 1764 of the NS3/NS4region of HCV type 3 (more particularly for new subtypes 3a sequences),and subtype 5a, as show in FIGS. 7 or 11;

new sequences spanning amino acid positions 2645 to 2757 of the NS5Bregion of HCV subtype 2d, type 3 (more particularly for new subtypes 3aand 3c), new type 4 subtypes (more particularly subtypes 4a, 4e, 4f, 4g,4h, 4i and 4j) and subtype 5a, as shown in FIG. 2.

Using the LiPA system mentioned above, Brazilian blood donors with hightiter type 3 hepatitis C virus, Gabonese patients with high-titer type 4hepatitis C virus, and a Belgian patient with high-titer HCV type 5infection were selected. Nucleotide sequences in the core, E1, NS5 andNS4 regions which have not yet been reported before, were analyzed inthe frame of the invention. Coding sequences (with the exception of thecore region) of any type 4 isolate are reported for the fist time in thepresent invention. The NS5b region was also analyzed for die new type 3isolates. After having determined the NS5b sequences, comparison withthe Ta and Tb subtypes described by Mori et al. (1992) was possible, andthe type 3 sequences could be identified as type 3a genotypes. The newtype 4 isolates segregated into 10 subtypes, based on homologiesobtained in the NS5 and E1 regions. New type 2 and 3 sequences couldalso be distinguished from previously described type 2 or 3 subtypesfrom sera collected in Belgium and the Netherlands.

The term “polynucleic acid” refers to a single stranded or doublestranded nucleic acid sequence which may contain at least 5 contiguousnucleotides to the complete nucleotide sequence (f.i. at least 6, 7, 8,9, 10, 11, 12, 13, 14, 15 or more contiguous nucleotides). A polynucleicacid which is up till about 100 nucleotides in length is often alsoreferred to as an oligonucleotide. A polynucleic acid may consist ofdeoxyribonucleotides or ribonucleotides, nucleotide analogues ormodified nucleotides, or may have been adapted for therapeutic purposes.A polynucleic acid may also comprise a double stranded cDNA clone whichcan be used for cloning purposes, or for in vivo therapy, orprophylaxis.

The term “polynucleic acid composition” refers to any kind ofcomposition comprising essentially said polynucleic acids. Saidcomposition may be of a diagnostic or a therapeutic nature.

The expression “nucleotides corresponding to” refers to nucleotideswhich are homologous or complementary to an indicated nucleotidesequence or region within a specific HCV sequence.

The term “coding region” corresponds to the region of the HCV genomethat encodes the HCV polyprotein. In fact, it comprises the completegenome with the exception of the 5′ untranslated region and 3′untranslated region.

The term “HCV polyprotein” refers to the HCV polyprotein of the HCV-Jisolate (Kato et al., 1990). The adenine residue at position 330 (Katoet al., 1990) is the first residue of the ATG codon that initiate thelong HCV polyprotein of 3010 amino acids in HCV-J and other type 1bisolates, and of 3011 amino acids in HCV-1 and other type 1a isolates,and of 3033 amino acids in type 2 isolates HC-J6 and HC-J8 (Okamoto etal., 1992).

This adenine is designated as position 1 at the nucleic acid level, andthis methionine is designated as position 1 at the amino acid level, inthe present invention. As type 1a isolates contain 1 extra amino acid inthe NS5a region, coding sequences of type 1a and 1b have identicalnumbering in the Core, E1, NS3, and NS4 region, but will differ in theNS5b region as indicated in Table 1. Type 2 isolates have 4 extra aminoacids in the E2 region, and 17 or 18 extra amino acids in the NS5 regioncompared to type 1 isolates, and will differ in numbering from type 1isolates in the NS3/4 region and NS5b regions as ted in Table 1.

TABLE 1 Positions Positions Positions Positions described in describedfor described for described for the HCV-J HCV-1 HC-J6, HC-J8 present(Kato et al., (Choo et al., (Okamoto et Region invention* 1990) 1991)al., 1992) Nucleotides NS5b 8023/8235 8352/8564 8026/8238 8433/86457932/8271 8261/8600 7935/8274 8342/8681 NS3/4 4664/5292 4993/56214664/5292 5017/5645 4664/4730 4993/5059 4664/4730 5017/5083 4892/52925221/5621 4892/5292 5245/5645 3856/4209 4185/4528 3856/4209 4209/47624936/5292 5265/5621 4936/5292 5289/5645 coding  330/9359   1/9033 342/9439 region of present invention Amino NS5b 2675/2745 2675/27452676/2746 2698/2768 Acids 2645/2757 2645/2757 2646/2758 2668/2780 NS3/41556/1764 1556/1764 1556/1764 1560/1768 1286/1403 1286/1403 1286/14031290/1407 1646/1764 1646/1764 1646/1764 1650/1768

Table 1: Comparison of the HCV nucleotide and amino acid numberingsystem used in the present invention (*) with the numbering used forother prototype isolates. For example, 8352/8564 indicates the regiondesignated by the numbering from nucleotide 8352 to nucleotide 8564 asdescribed by Kato et al. (1990). Since the numbering system of thepresent invention starts at the polyprotein initiation site, the 329nucleotides of the 5′ untranslated region described by Kato et al.(1990) have to be substracted, and the corresponding region is numberedfrom nucleotide 8023 (“8352-329”) to 8235 (“8564-329”).

The term “HCV type” corresponds to a group of HCV isolates of which thecomplete genome shows more than 74% homology at the nucleic acid levelsor of which the NS5 region between nucleotide positions 7932 and 8271shows more than 74% homology at the nucleic acid level, or of which thecomplete HCV polyprotein shows more than 78% homology at the amino acidlevel, or of which the NS5 region between amino acids at positions 2645and 2757 shows more than 80% homology at the amino acid level, topolyproteins of the other isolates of the group, with said numberingbeginning at the first ATG codon or first methionine of the long HCVpolyprotein of the HCV-J isolate (Kato et al., 1990). Isolates belongingto different type of HCV exhibit homologies, over the complete genome,of less than 74% at the nucleic acid level and less than 78% at theamino acid level. Isolates belonging to the same type usually showhomologies of about 92 to 95% at the nucleic acid level and 95 to 96% atthe amino acid level when belonging to the same subtype, and thosebelonging to the same type but different subtypes preferably showhomologies of about 79% at the nucleic acid level and 85-86% at theamino acid level.

More preferably the definition of HCV types is concluded from theclassification of HCV isolates according to their nucleotide distancescalculated as detailed below:

(1) based on phylogenetic analysis of nucleic acid sequences in the NS5bregion between nucleotides 7935 and 8274 (Choo et al., 1991) or 8261 and8600 (Kato et al., 1990) or 8342 and 8681 (Okamoto et al., 1991),isolates belonging to the same HCV type show nucleotide distances ofless than 0.34, usually less than 0.33, and more usually of less than0.32, and isolates belonging to the same subtype show nucleotidedistances of less than 0.135, usually of less than 0.13, and moreusually of less than 0.125, and consequently isolates belonging to thesame type but different subtypes show nucleotide distances ranging from0.135 to 0.34, usually ranging from 0.1384 to 0.2477, and more usuallyranging from 0.15 to 0.32, and isolates belonging to different HCV typesshow nucleotide distances greater than 0.34, usually greater that 0.35,and more usually of greater than 0.358, more usually ranging from 0.1384to 0.2977.

(2) based on phylogenetic analysis of nucleic acid sequences in thecore/E1 region between nucleotides 378 and 957, isolates belonging tothe same HCV type show nucleotide distances of less than 0.38, usuallyof less than 0.37, and more usually of less than 0.364, and isolatesbelonging to the same subtype show nucleotide distances of less than0.17, usually of less than 0.16, and more usually of less than 0.15,more usually less than 0.135, more usually less than 0.134, andconsequently isolates belonging to the same type but different subtypesshow nucleotide distances ranging from 0.15 to 0.38, usually rangingfrom 0.16 to 0.37, and more usually ranging from 0.17 to 0.36, moreusually ranging from 0.133 to 0.379, and isolate belonging to differentHCV types show nucleotide distances greater than 0.34, 0.35, 0.36,usually more than 0.365, and more usually of greater than 0.37.

(3) based on phylogeneic analysis of nucleic acid sequences in theNS3/NS4 region between nucleotides 4664 and 5292 (Choo et al., 1991) orbet nucleotides 4993 and 5621 (Kato et al., 1990) or between nucleotides5017 and 5645 (Okamoto et al., 1991), isolates belonging to the same HCVtype show nucleotide distances of less than 0.35, usually of less than0.34, and more usually of less than 0.33, and isolates belonging to thesame subtype show nucleotide distances of less than 0.19, usually ofless than 0.18, and more usually of less than 0.17, and consequentlyisolates belonging to the same type but different subtypes shownucleotide distances ranging from 0.17 to 0.35, usually ranging from0.18 to 0.34, and more usually ranging from 0.19 to 0.33, and isolatesbelonging to different HCV types show nucleotide distances greater than0.33, usually greater than 0.34, and more usually of greater than 0.35.

TABLE 2 Molecular evolutionary distances Core/E1 E1 NS5B NS5B Region 579bp 384 bp 340 bp 222 bp Isolates* 0.0017-0.1347 0.0026-0.20310.0003-0.1151 0.000-0.1323 (0.0750 ± 0.0245) (0.0969 ± 0.0289) (0.0637 ±0.0229) (0.0607 ± 0.0205) Subtypes* 0.1330-0.3794 0.1645-0.48690.1384-0.2977 0.117-0.3538 (0.2786 ± 0.0363) (0.3761 ± 0.0433) (0.2219 ±0.0341) (0.2391 ± 0.0399) Types* 0.3479-0.6306 0.4309-0.95610.3581-0.6670 0.3457-0.7471 (0.4703 ± 0.0525) (0.6308 ± 0.0928) (0.4994± 0.0495) (0.5295 ± 0.0627) *Figures created by the PHYLIP programDNADIST are expressed as minimum to maximum (average ± standarddeviation). Phylogenic distances for isolates belonging to the samesubtype (‘isolates’), to different subtypes of the same type(‘subtypes’), and to different types (‘types’) are given.

In a comparative phylogenetic analysis of available sequences, ranges ofmolecular evolutionary distances for different regions of the genomewere calculated, based on 19,781 pairwise comparisons by means of theDNA DIST program of the phylogeny inference package PHYLIP version 3.5C(Felsenstein, 1993). The results are shown in Table 2 and indicate thatalthough the majority of distances obtained in each region fit withclassification of a certain isolate, only the ranges obtained in the 340bp NS5B-region are non-overlapping and therefore conclusive. However, aswas performed in the present invention, it is preferable to obtainsequence information from at least 2 regions before final classificationof a given isolate.

Designation of a number to the different types of HCV and HCV typesnomenclature is based on chronological discovery of the different types.The numbering system used in the present invention might still fluctuateaccording to international conventions or guidelines. For example, “type4” might be changed into “type 5” or “type 6”.

The term “subtype” corresponds to a group of HCV isolates of which thecomplete polyprotein shows a homology of more than 90% both at thenucleic acid and amino acid levels, or of which the NS5 region betweennucleotide positions 7932 and 8271 shows a homology of more than 90% atthe nucleic acid level to the corresponding parts of the genomes of theother isolates of the same group, with said numbering beginning with theadenine residue of the initiation codon of the HCV polyprotein. Isolatesbelonging to the same type but different subtypes of HCV show homologiesof more than 74% at the nucleic acid level and of more than 78% at theamino acid level.

The term “BR36 subgroup” refers to a group of type 3a HCV isolates(BR36, BR33, BR34) that are 95%, preferably 95.5%, most preferably 96%homologous to the sequences as represented in SEQ ID NO 1, 3, 5, 7, 9,11 in the NS5b region from position 8023 to 8235.

It is to be understood that extremely variable regions like the E1, E2and NS4 regions will exhibit lower homologies than the average homologyof the complete genome of the polyprotein

Using these criteria, HCV isolates can be classified into at least 6types. Several subtypes can clearly be distinguished in types 1, 2, 3and 4: 1a, 1b, 2a, 2b, 2c, 2d, 3a, 3b, 4a, 4 b, 4c, 4d, 4e, 4f, 4g, 4h,4i and 4j based on homologies of the 5′ UR and coding regions includingthe part of NS5 between positions 7932 and 8271. An overview of most ofthe reported isolates and their proposed classification according to thetyping system of the present invention as well as other proposedclassifications is presented in Table 3.

TABLE 3 HCV CLASSIFICATION OKA- MOTO MORI NAKAO CHA PROTOTYPE 1a I I PtGI HCV-1, HCV-H, HC-J1 1b II II KI GII HCV-J, HCV-BK, HCV-T, HC-JK1, HC-J4, HCV-CHINA 1c HC-G9 2a III III K2a GIII HC-J6 2b IV IV K2b GIII HC-J82c S83, ARG6, ARG8, I10, T983 2d NE92 3a V V K3 GIV E-b1, Ta, BR36,BR33, HD10, NZL1 3b VI K3 GIV HCV-TR, Tb 3c BE98 4a Z4, GB809-4 4b Z1 4cGB116, GB358, GB215, Z6, Z7 4d DK13 4e GB809-2, CAM600, CAM736 4fCAM622, CAM627 4g GB549 4h GB438 4i CAR4/1205 4j CAR1/501 4k EG29 5a GVSA3, SA4, SA1, SA7, SA11, BE95 6a HK1, HK2, HK3, HK4

The term “complement” refers to a nucleotide sequence which iscomplementary to an indicated sequence and which is able to hybridize tothe indicated sequences.

The composition of the invention can comprise many combinations. By wayof example, die composition of the invention can comprise:

two (or more) nucleic acids from the same region or,

two nucleic acids (or more), respectively from different regions, forthe same isolate or for different isolates,

or nucleic acids from the same regions and from at least two differentregions (for the same isolate or for different isolate).

The present invention related more particularly to a polynucleic acidcomposition as defined above, wherein said polynucleic acid correspondsto a nucleotide sequence selected from any of the following HCV type 3genomic sequences:

an HCV genomic sequence having a homology of at least 67%, preferablymore than 69%, more preferably 71%, even more preferably more than 73%,or most preferably more than 76% to any of the sequences as representedin SEQ ID NO 13, 15, 17, 19, 21, 23, 25 or 27 (HD10, BR36 or BR33sequences) in the region spanning positions 417 to 957 of the Core/E1region as shown in FIG. 4;

an HCV genomic sequence having a homology of at least 65%, preferablymore than 67%, preferably more than 69%, even preferably more than 70%,most preferably more than 74% to any of the sequences as represented inSEQ ID NO 13, 15, 17, 19, 21, 23, 25 or 27 (HD10, BR36 or BR33sequences) in the region spacing positions 574 to 957 of the E1 regionas shown in FIG. 4;

an HCV genomic sequence as having a homology of at least 79%, morepreferably at least 81%, most preferably more than 83% or more to any ofthe sequences as represented in SEQ ID NO 147 (representing positions 1to 346 of the Core region of HCV type 3c, sequence BE98) in the regionspanning positions 1 to 378 of the Core region as shown in FIG. 3;

an HCV genomic sequence of HVC type 3a having a homology of at least74%, more preferably at least 76, 7, most preferably more than 78% ormore to any of the sequences as represented in SEQ ID NO 13, 15, 17, 19,21, 23, 25 or 27 (HD10, BR36 or BR33 sequences) in the region spanningpositions 417 to 957 in the Core/E1 region as shown in FIG. 4;

an HCV genomic sequence of HCV type 3a as having a homology of at least74%, preferably more than 76%, most preferably 78% or more to any of thesequences as represented in SEQ ID NO 13, 15, 17, 19, 21, 23, 25 or 27(HD10, BR36 or BR33 sequences) in the region spanning positions 574 to957 in the E1 region as shown in FIG. 4;

an HCV genomic sequence as having a homology of more than 73.5%,preferably more than 74%, most preferably 75% homology to the sequenceas represented in SEQ ID NO 29 (HCC153 sequence) in the region spanningpositions 4664 to 4730 of the NS3 region as shown in FIG. 6;

an HCV genomic sequence having a homology of more than 70%, preferablymore than 72%, most preferably more than 74% homology to any of thesequences as represented in SEQ ID NO 29, 31, 33, 35, 37 or 39 (HCC153,HD10, BR36 sequences) in the region spanning positions 4892 to 5292 inthe NS3/NS4 region as shown in FIG. 6 or 10;

an HCV genomic sequence of the BR36 subgroup of HCV type 3a as having ahomology of more than 95%, preferably 95, 5%, most preferably 96%homology to any of the sequences as represented in SEQ ID NO 5, 7, 1, 3,9 or 11(BR34, BR33, BR36 sequences) in the region spanning positions8023 to 8235 of the NS5 region as shown in FIG. 1;

an HCV genomic sequence of the BR36 subgroup of HCV type 3a as having ahomology of more than 96%, preferably 96.5%, most preferably 97%homology to any of the sequences as represented in SEQ ID NO 5, 7, 1, 3,9 or 11 (BR34, BR33, BR36 sequences) in the region spanning positions8023 to 8192 of the NS5B region as shown in FIG. 1;

an HCV genomic sequence of HCV type 3c being characterized as having ahomology of more than 79%, more preferably more than 81%, and mostpreferably more than 83% to the sequence as represented in SEQ ID NO 149(BE98 sequence) in the region spanning positions 7932 to 8271 in theNS5B region as shown in FIG. 1.

Preferentially the above-mentioned genomic HCV sequences depictsequences from the coding regions of all the above-mentioned sequences.

According to the nucleotide distance classification system (with saidnucleotide distances being calculated as explained above), saidsequences of said composition are selected from:

an HCV genomic sequence being characterized as having a nucleotidedistance of less than 0.44, preferably of less than 0.40, mostpreferably of less than 0.36 to any of the sequences as represented inSEQ ID NO 13, 15, 17, 19, 21, 23, 25 or 27 in the region spanningpositions 417 to 957 of the Core/E1 region as shown in FIG. 4;

an HCV genomic sequence being characterized having a nucleotide distanceof less than 0.53, preferably less than 0.49, most preferably of lessthan 0.45 to any of the sequence as represented in SEQ ID NO 19, 21, 23,25 or 27 in the region spanning positions 574 to 957 of the E1 region asshown in FIG. 4;

an HCV genomic sequent charaterized having a nucleotide distance of lessthan 0.15, preferably less than 0.13, and most preferably less than 0.11to any of the sequences as represented in SEQ ID NO 147 in the regionspanning positions 1 to 378 of the Core region as shown in FIG. 3;

an HCV genomic sequence of HVC type 3a being characterized as having anucleotide distance of less than 0.3, preferably less than 0.26, mostpreferably of less than 0.22 to any of the sequences as represented inSEQ ID NO 13, 15, 17, 19, 21, 23, 25 or 27 in the region spanningpositions 417 to 957 in the Core/E1 region as shown in FIG. 4;

an HCV genomic sequence of HCV type 3a being characterized as having anucleotide distance of less than 0.35, preferably less than 0.31, mostpreferably of less than 0.27 to any of the sequences as represented inSEQ ID NO 13, 15, 17, 19, 21, 23, 25 or 27 in the region spanningpositions 574 to 957 in the E1 region as shown in FIG. 4;

an HCV genomic sequence of the BR36 subgroup of HCV type 3a beingcharacterized as having a nucleotide sequence of less than 0.0423,preferably less than 0.042, preferably less than 0.0362 to any of thesequences as represented in SEQ ID NO 5, 7, 1, 3, 9 or 11 in the regionspanning positions 8023 to 8235 of the NS5 region as shown in FIG. 1;

an HCV genomic sequence of HCV Ape 3c being characterized as having anucleotide distance of less than 0.255, preferably of less than 0.25,more preferably of less than 0.21, most preferably of less than 0.17 tothe sequence as represented in SEQ ID NO 149 in the region spanningpositions 7932 to 8271 in the NS5B region as shown in FIG. 1.

In the present application, the E1 sequences encoding the antigenicectodomain of the E1 protein, which does not overlap the carboxyterminalsignal-anchor sequences of E1 disclosed by Cha et al. (1992; WO92/19743), in addition to the NS4 epitope region, and a part of the NS5region are disclosed for 4 different isolates: BR33, BR34, BR36, HCC153and HD10, all belonging to type 3a (SEQ ID NO 1, 3, 5, 7, 9, 11, 13 ,15, 17, 19, 21, 23, 25, 27, 29, 31, 35, 37 or 39).

Also within the present invention are new subtype 3c sequences (SEQ IDNO 147, 149 of the isolate BE98 in the Core and NS5 regions (see FIGS. 3and 1).

Finally the present invention also relates to a new subtype 3a sequenceas represented in SEQ ID NO 217 (see FIG. 1)

Also included within the present invention are sequence variants of thepolynucleic acids as selected from any of the nucleotide sequences asgiven in any of the above mentioned SEQ ID numbers, with said sequencevariants containing either deletions and/or insertions of one or morenucleotides, mainly at the extremities of oligonucleotide (either 3′ or5′), or substitutions of some non-essential nucleotides by others(including modified nucleotides an/or inosine), for example, a type 1 or2 sequence might be modified into a type 3 sequence by replacing somenucleotides of the type 1 or 2 sequence with type-specific nucleotidesof type 3 as shown in FIG. 1 (NS5 region), FIG. 3 (Core region), FIG. 4(Core/E1 region), FIGS. 6 and 10 (NS31/NS4 region).

According to another embodiment, the present invention relates to apolynucleic acid composition as defined above, wherein said polynucleicacids correspond to a nucleotide sequence selected from any of thefollowing HCV type 5 genomic sequences:

an HCV genomic sequence as having a homology of more than 85%,preferably more than 86%, most preferably more than 87% homology to anyof the sequences as represented in SEQ ID NO 41, 43, 45, 47, 49, 51, 53(PC sequences) or 151 (BE95 sequence) in the region spanning positions 1to 573 of the Core region as shown in FIGS. 9 and 3;

an HCV genomic sequence as having a homology of more than 61%,preferably more than 63%, more preferably more than 65% homology, evenmore preferably more than 66% homology and most preferably more than 67%homology (f.i. 69 and 71%) to any of the sequences as represented in SEQID NO 41, 43, 45, 47, 49, 51, 53 (PC sequences), 153 or 155 (BE95, BE100sequences) in the region spanning positions 574 to 957 of the E1 regionas shown in FIG. 4;

an HCV genomic sequence having a homology of more than 76.5%, preferablyof more than 77%, most preferably of more than 78% homology with any ofthe sequences as represented in SEQ ID NO 55, 57, 197 or 199 (PCsequences) in the region spanning positions 3856 to 4209 of the NS3region as shown in FIG. 6 or 10;

an HCV genomic sequence having a homology of more than 68%, preferablyof more the 70%, most preferably of more than 72% homology with thesequence as represented in SEQ ID NO 157 (BFE95 sequence) in the regionspanning positions 980 to 1179 of the E1/E2 region as shown in FIG. 13;

an HCV genomic sequence having a homology of more than 57%, preferablymore than 59%, most preferably more than 61% homology to any of thesequences as represented in SEQ ID NO 59 or 61 (PC sequences) in theregion s g positions 4936 to 5296 of the NS4 region as shown in FIGS. 6or 10;

an HCV genomic sequence as having a homology of more than 93%,preferably more than 93.5%, most preferably more than 947% homology toany of the sequences as represented in SEQ ID NO 159 or 161 (BE95 orBE96 sequences) in the region spanning positions 7932 to 8271 of theNS5B region as shown in FIG. 1.

Preferentially the above-mentioned genomic HCV sequences depictsequences from die coding regions of all the above-mentioned sequences.

According to the nucleotide distance classification system (with saidnucleotide distances being calculated as explained above), said sequenceof said composition are selected from:

a nucleotide distance of less than 0.53, preferably less than 0.51, morepreferably Less than 0.49 for the E1 region to the type 5 sequencesdepicted above;

a nucleotide distance of less than 0.3, preferably less than 0.28, morepreferably of less tan 0.26 for the Core region to the type 5 sequencesdepicted above;

a nucleotide distance of less than 0.072, preferably less than 0.071,more preferably less than 0.070 for the NS5B region to the type 5sequences as depicted above.

Isolates with similar sequences in the 5′UR to a group of isolatesincluding SA1, SA3, and SA7 described in the 5′UR by Bukh et al. (1992),have been reported and described in the 5′UR and NS5 region as group Vby Cha et al. (1992; WO 92/19743). This group of isolates belongs totype 5a as described in the present invention (SEQ ID NO 41, 43, 45, 47,49, 51, 53, 55, 57, 59, 61, 151, 153, 155, 157, 159, 161, 197 and 199).

Also included within the present invention are sequence variants of thepolynucleic acids as selected from any of the nucleotide sequences asgiven in any of the above given SEQ ID numbers with said sequencevariants containing either deletion and/or insertions of one or morenucleotides, mainly at the extremities of oligonucleotide (either 3′ or5′), or substitutions of some non-essential nucleotides (i.e.nucleotides not essential to discriminate between different genotypes ofHCV) by others (including modified nucleotides an/or inosine), forexample, a type 1 or 2 sequence might be modified into a type 5 sequenceby replacing some nucleotides of the type 1 or 2 sequence withtype-specific nucleotides of type 5 as shown in FIG. 3 (Core region),FIG. 4 (Core/E1 region). FIG. 10 (NS3/NS4 region), FIG. 14 (E1/E2region).

Another group of isolates including BU74 and BU79 having similarsequences in the 5′UR to isolates including Z6 and Z7 as described inthe 5′UR by Bukh et al. (1992), have been described in the 5′UR andclassified as a new type 4 by the inventors of this application (Stuyveret al., 1993). Coding sequences, including core, E1 and N55 sequences ofseveral new Gabonese isolates belonging to this group, are disclosed inthe present invention (SEQ ID NO 106, 108, 110, 112, 114, 116, 118, 120and 122).

According to yet another embodiment, the present invention Tess to acomposition as defined above, wherein said polynucleic acids correspondto a nucleotide sequence selected from any of the following HCV type 4genomic sequences:

an HCV genomic sequence having a homology of more than 66%, preferablymore than 68%, most preferably more than 70% homology in the E1 regionspanning positions 574 to 957 to any of the sequences as represented inSEQ ID) NO 118, 120 or 122 (GB358, GB549, GB809 sequences) as shown inFIG. 4:

an HCV genomic sequence having a homology of more than 71%, preferablymore than 72%, most preferably more than 74% homology to any of thesequences as represented in SEQ ID NO 118, 120 or 122 (GB358, GB549,GB809 sequences) in the region spanning positions 379 to 957 of the E1region as shown in FIG. 4;

an HCV genomic sequence having a homology of more than 92%, preferablymore than 93%, most preferably more than 94% homology to any of thesequences as represented in SEQ ID NO 163 or 165 (GB809, CAM600sequences) in the region spanning positions to 378 of the Core/E1 regionas shown in FIG. 4;

an HCV genomic sequence (subtype 4c) having a homology of more than 85%,preferably more than 86%, more preferably more than 86.5% homology, mostpreferably more than 87, more the 88 or more than 89% homology to any ofthe sequences as represented in SEQ ID NO 183, 185 or 187 (GB116, GB215,GB809 sequences) in the region spanning positions 379 to 957 of the E1region as shown in FIG. 4;

an HCV genomic sequence (subtype 4a) having a homology of more than 81%,preferably more than 83%, most preferably more than 85% homology to thesequence as represented in SEQ ID NO 189 (GB908 sequence) in the regionspanning positions 379 to 957 of the E1 region as shown in FIG. 4;

an HCV genomic sequence (subtype 4e) having a homology of more than 85%,preferably more than 87%, most preferably more than 89% homology w anyof the sequences as represented in SEQ ID NO 167 or 169 (CAM600, GB908sequences) in the region spanning positions 379 to 957 of the E1 regionas shown in FIG. 4;

an HCV genomic sequence (subtype 4f) having a homology of more than 79%,preferably more than 81%, most preferably more than 83% homology lo anyof the sequences as represented in SEQ ID NO 171 or 173 (CAMG22, CAMG27sequences) in the region spanning positions 379 to 957 of the E1 regionas shown in FIG. 4;

an HCV genomic sequence (subtype 4g) having a homology of more than 84%,preferably more than 86%, most preferably more than 88% homology to thesequence as represented in SEQ ID NO 175 (GB549 sequence) in the regionspanning positions 379 to 957 of the E1 region as shown in FIG. 4;

an HCV genomic sequence (subtype 4h) having a homology of more than 83%,preferably more than 85%, most preferably more than 87% homology to thesequence as represented in SEQ ID NO 177 (GB438 sequence) in the regionspanning positions 379 to 957 of the E1 region as shown in FIG. 4;

an HCV genomic sequence (subtype 4i) as having a homology of more than76%, preferably more than 78%, most preferably more than 80% homology tothe sequence as represented in SEQ ID NO 179 (CAR4/1205 sequence) in theregion spanning positions 379 to 957 of the E1 region as shown in FIG.4;

an HCV genomic sequence (subtype 4j?) having a homology of more than 84%preferably more than 86%, most preferably more than 88% homology to thesequence as represented in SEQ ID NO 181 (CAR4/901 sequence) in theregion spanning positions 379 to 957 of the E1 region as shown in FIG.4;

an HCV genomic sequence as having a homology of more than 73%,preferably more than 75%, most preferably more than 77% homology to anyof the sequences as represented in SEQ ID NO 106, 108, 110, 112, 114, or116 (GB48, GB116, GB215, GB358, GB549, GB809 sequences) in the regionspanning positions 7932 to 8271 of the NS5 region as shown in FIG. 1:

an HCV genomic sequence (subtype 4c) having a homology of more than 88%,preferably more than 89%, most preferably more than 90% homology to anyof the sequences as represented in SEQ ID NO 106, 108, 110, or 112(GB48, GB116, GB215, GB358 sequences) in the region spanning positions7932 to 8271 of the NS5 region as shown in FIG. 1;

an HCV genomic sequence (subtype 4e) having a homology of more than 88%,preferably more than 89%, most preferably more than 90% homology to anyof the sequences as represented in SEQ ID NO 116 or 201 (GB809 or CAM600 sequences) in the region spanning positions 7932 to 8271 of the NS5region as shown in FIG. 1:

an HCV genomic sequence (subtype 4f) having a homology of more than 87%,preferably more than 89%, most preferably more than 90% homology to thesequence as represented in SEQ ID NO 203 (CAMG22 sequence) in the regionSpanning positions 7932 to 8271 of the NS5 region as shown in FIG. 1;

an HCV genomic sequence (subtype 4g) as having a homology of more than85%, preferably more than 87%, most preferably more than 89% homology tothe sequence as represented in SEQ ID NO 114 (GB549 sequence) in theregion spanning positions 7932 to 8271 of the NS5 region as shown inFIG. 1;

an HCV genomic sequence (subtype 4h) as having a homology of more than86%, preferably more than 87%, more preferably more than 88% homology,more preferably more than 89% homology to the sequence as represented inSEQ ID NO 207 (GB437 sequence) in the region spanning positions 7932 to8271 of the NS5 region as shown in FIG. 1:

an HCV genomic sequence (subtype 4i) having a homology of more than 84%,preferably more than 86%, most preferably more than 88% homology to thesequence as represented in SEQ ID NO 209 (CAR4/1205 sequence) in theregion spanning positions 7932 to 8271 of the NS5 region as shown inFIG. 1;

an HCV genomic sequence (subtype 4j) having a homology of more than 81%,preferably more than 83%, most preferably more than 85% homology to thesequence as represented in SEQ ID NO 211 (CAR1/501 sequence) in theregion spanning positions 7932 to 8271 of the NS5 region as shown inFIG. 1.

Preferentially the above-mentioned genomic HCV sequences depictsequences from the coding regions of all the above-mentioned sequences.

According to the nucleotide distance classification system (with saidnucleotide distances being calculated as explained above), saidsequences of said composition are selected from:

an HCV genomic sequence (type 4) being characterized as having anucleotide distance of less than 0.52, 0.50, 0.4880, 0.46, 0.44, 0.43 ormost preferably less than 0.42 in the region spanning positions 574 to957 to any of the sequences as represented in SEQ ID NO 118, 120 or 122in the region spanning positions 1 to 957 of the Core/E1 region as shownin FIG. 4;

an HCV genomic sequence (type 4) being characterized as having anucleotide distance of less than 0.39, 0.36 0.34 0.32 or most preferablyless than 0.31 to any of the sequences as represented in SEQ ID NO 118,120 or 122 in the region spanning positions 379 to 957 of the E1 regionas shown in FIG. 4;

an HCV genomic sequence (subtype 4c) being characterized as having anucleotide distance of less than 0.27, 0.26, 0.24, 0.22, 0.20, 0.18,0.17, 0.162, 0.16 or most preferably less than 0.15 to any of thesequences as represented in SEQ ID NO 183, 185 or 187 in the regionspanning positions 379 to 957 of the E1 region as shown in FIG. 4;

an HCV genomic sequence (subtype 4a) being characterized as having anucleotide distance of less than 0.30, 0.28, 0.26, 0.24, 0.22, 0.21 ormost preferably of less than 0.205 to the sequence as represented in SEQID NO 189 in the region spanning positions 379 to 957 of the E1 regionas shown in FIG. 4;

an HCV genomic sequence (subtype 4e) being characterized as having anucleotide distance of less than 0.26, 0.25, 0.23, 0.21, 0.19, 0.17,0.165, most preferably less than 0.16 to any of the sequences asrepresent in SEQ ID NO 167 or 169 in the region spanning positions 379to 957 of the E1 region as shown in FIG. 4;

an HCV genomic sequence (sub type 4f) being characterized as having anucleotide distance of less than 0.26, 0.24, 0.22, 0.20, 0.18, 0.16,0.15 or most preferably less than 0.14 to any of the sequences asrepresented in SEQ ID NO 171 or 173 in the region spanning positions 379to 957 of the E1 region as shown in FIG. 4;

an HCV genomic sequence (subtype 4g) being characterized as having anucleotide distance of less than 0.20, 0.19, 0.18, 0.17 or mostpreferably of less than 0.16 to the sequence as represented in SEQ ID NO175 in the region spanning positions 379 to 957 of the E1 region asshown in FIG. 4;

an HCV genomic sequence (subtype 4h) being characterized as having anucleotide distance of less than 0.20, 0.19, 0.18, 0.17 and mostpreferably of less than 0.16 to the sequence as represented in SEQ ID NO177 in the region spanning positions 379 to 957 of the E1 region asshown in FIG. 4;

an HCV genomic sequence (subtype 4i) being characterized as having anucleotide distance of less than 0.27, 0.25, 0.23, 0.21 and preferablyless than 0.16 to the sequence as represented in SEQ ID NO 179 in theregion spanning positions 379 to 957 of the E1 region as shown in FIG.4;

an HCV genomic sequence (subtype 4j?) being characterized as having anucleotide distance of less than 0.19, 0.18, 0.17, 0.165 and mostpreferably of less than 0.6 to the sequence as represented in SEQ ID NO181 in the region spanning positions 379 to 957 of the E1 region asshown in FIG. 4;

an HCV genomic sequence (type 4) being characterized as having anucleotide distance of less tan 0.35, 0.34, 0.32 and most preferably ofless than 0.30 to any of the sequences as represented in SEQ ID NO 106,108, 110, 112, 114, or 116 in the region spanning positions 7932 to 8271of the NS5 region as shown in FIG. 1;

an HCV genomic sequence (subtype 4c) being characterized as having anucleotide distance of less than 0.18, 0.16, 0.14, 0.135, 0.13, 0.1275or most preferably less than 0.125 to any of the sequences asrepresented in SEQ ID NO 106, 108, 110, or 112 in the region spanningpositions 7932 to 8271 of the NS5 region as shown in FIG. 1;

an HCV genomic sequence (subtype 4e) being characterized as having anucleotide distance of less than 0.15, 0.14, 0.135, 0.13 and mostpreferably of less than 0.125 to any of the sequences as represented inSEQ ID NO 116 or 201 in the region spuming positions 7932 to 8271 of theNS5 region as shown in FIG. 1;

an HCV genomic sequence (subtype 4f) being characterized as having anucleotide distance of less than 0.15, 0.14, 0.135, 0.13 or mostpreferably less than 0.125 to the sequence as represented in SEQ ID NO203 in the region spanning positions 7932 to 8271 of the NS5 region asshown in FIG. 1;

an HCV genomic sequence (subtype 4g) being characterized as having anucleotide distance of less than 0.17, 0.16, 0.15, 0.14, 0.13 or mostpreferably less than 0.5 to the sequence as represented in SEQ ID NO 114in the region spanking positions 7932 to 8271 of the NS5 region as shownin FIG. 1;

an HCV genomic sequence (subtype 4h) being characterized as having anucleotide distance of less than 0.155, 0.15, 0.145, 0.14, 0.135, 0.13or most preferably less than 0.125 to the sequence as represented in SEQID NO 207 in the region spanning positions 7932 to 8271 of the NS5region as shown in FIG. 1;

an HCV genomic sequence (subtype 4i) being characterized as having anucleotide distance of less than 0.17, 0.16, 0.15, 0.14, 0.13 or mostpreferably of less than 0.125 to the sequence as represented in SEQ IDNO 209 in the region spanning positions 7932 to 8271 of the NS5 regionas shown in FIG. 1;

an HCV genomic sequence (subtype 4j) being characterized as having anucleotide distance of less than 0.21, 0.20, 0.19, 0.18, 0.17, 0.16,0.15, 0.14, 0.13 and most preferably of less than 0.125 to the sequenceas represented in SEQ ID NO 211 in the region spanning positions 7932 to8271 of the NS5 region as shown i FIG. 1.

Also included within the present invention are sequence variants of thepolynucleic acids as selected from any of the nucleotide sequences asgiven in any of the above given SEQ ID numbers with said sequencevariants containing either deletion and/or insertions of one or morenucleotides, mainly at the extremities of oligonucleotide (either 3′ or5′), or substitutions of some non essay nucleotides (i.e. nucleotidesnot essential to dilute between different genotypes of HCV) by others(including modified nucleotides an/or inosine), for example, a type 1 or2 sequence might be modified into a type 4 sequence by replacing somenucleotides of the type 1 or 2 sequence with type-specific nucleotidesof type 4 as shown in FIG. 3 (Core region), FIG. 4 (Core/E1 region),FIG. 10 (NS3/NS4 region), FIG. 14 (E1/E2 region).

The present invention also relates to a sequence as represented in SEQID NO 193 (GB724 sequence).

After aligning NS5 or E1 sequences of G348, GB, 116, GB215, GB358, GB549and GB809, these isolates clearly segregated into 3 subtypes within type4 : GB48, GB116, GB215 and GB358 belong to the subtype designated 4c,GB549 to subtype 4g and GB809 to subtype 4e. In NS5, GB809 (subtype 4e)showed a higher nucleic acids homology to subtype 4c isolates(85.6-86.8%) than to GB549 (subtype 4g, 79.7%), while GB549 showedsimilar homologies to both other subtypes (78.8 to 80% to subtype 4c and79.7% to subtype 4e). In E1, subtype 4c showed equal nucleic acidhomologies of 75.2% to subtypes 4g and 4e while 4g and 4e were 78.4%homologous. At the amino acid level however, subtype 4e showed a normalhomology to subtype 4c (80.2%), while subtype 4g was more homologous to4c (83.3%) and 4e (84.1%).

According to yet another embodiment, the present invention relates to acomposition as defined above, wherein said polynucleic acids correspondto a nucleotide sequence selected from any of the following HCV type 2dgenomic sequences:

an HCV genomic sequence as having a homology of more than 78%,preferably more than 80%, most preferably more than 82% homology to thesequence as represented in SEQ ID NO (NE92) 143 in the region spanningpositions 379 to 957 of the Core/E1 region as shown in FIG. 4;

an HCV genomic sequence as having a homology of more than 74%,preferably more than 76%, most preferably more than 78% homology to thesequence as represented in SEQ ID NO 143 (NE92) in the region spanningpositions 574 to 957 as shown in FIG. 4;

an HCV genomic sequence as having a homology of more than 87%,preferably more than 89%, most preferably more than 91% homology to thesequence as represented in SEQ ID NO 145 (NE92) in the region spanningpositions 7932 to 8271 of the NS5B region as shown in FIG. 1.

Preferentially the above-mentioned genomic HCV sequences depictsequences from the coding regions of all the above-mentioned sequences.

According to the nucleotide distance classification system (with saidnucleotide distances being calculated as explained above), saidsequences of said composition are selected from:

a nucleotide distance of less than 0.32, preferably less than 0.31, morepreferably less than 0.30 for the E1 region (574 to 957) to any of theabove specified sequences;

a nucleotide distance of less than 0.08, preferably less than 0.07, morepreferably less than 0.06 for the Core region (1 to 378) to any of theabove given sequences

a nucleotide distance of less than 0.15, preferentially less than 0.13,more preferentially less than 0.12 for the NS5B region to any of theabove-specified sequences.

Polynucleic acid sequences according to the present invention which arehomologous to the sequences as represented by a SEQ ID NO can becharacterized and isolated according to any of the techniques known inthe art, such as amplification by means of type or subtype specificprimers, hybridization with type or subtype specific probes under moreor less stringent conditions, serological screening methods (seeexamples 4 and 11) or via the LiPA typing system.

Polynucleic acid sequences of the genomes indicated above from regionsnot yet depicted in the present examples, figures and sequence listingcan be obtained by any of the techniques known in the art, such asamplification techniques using suitable primers from the type or subtypespecific sequences of the present invention.

The present invention relates also to a composition as defined above,wherein said polynucleic acid is liable to act as a primer foramplifying the nucleic acid of a certain isolate belonging to thegenotype from which the primer is derived.

An example of a primer according to this embodiment of the invention isHCPr 152 as shown in table 7 (SEQ ID NO 79).

The term “primer” refers to a single stranded DNA oligonucleotidesequence capable of acting as a point of initiation for synthesis of aprimer extension product which is complementary to the nucleic acid sandto be copied. The length and the sequence of the primer must be suchthat they allow to prime the synthesis of the extension products.Preferably the primer is about 5-50 nucleotides. Specific length andsequence will depend on the complexity of the required DNA or RNAtargets, as well as on the conditions of or use such as temperature andionic strength.

The fact than amplification primers do not have to match exactly withcorresponding template sequence to warrant proper amplification is amplydocumented in the liters (Kwok et al., 1990).

The amplification method used can be either polymerase chain reaction(PCR, Saiki et al., 1988), ligase chain reaction (LCR; Lidgren et al.,1988; Wu & Wace, 1989; Barany, 1991), nucleic acid sequence-basedamplification (NASBA; Guatelli et al., 1990; Compton, 1991),transcription-based amplification system CTAS; Kwoh et al. 1989), stranddisplacement amplification (SDA; Duck, 1990; Walker et al., 1992) oramplification by means of Qβ replicase (Lizardi et al., 1988; Lomeli etal., 1989) or any other suitable method to amplify nucleic acidmolecules using primer extension. During amplification, the amplifiedproducts can be conveniently labelled either using labelled primers orby incorporating labelled nucleotides. Labels may be isotopic (³⁵P, ³⁵S,etc.) or non-isotopic (biotin, digoxigenin etc.). The amplificationreaction is repeated between 20 and 80 times, advantageously between 30and 50 times.

The present invention also relates to a composition as defined above,wherein said polynucleic acid is able to act as a hybridization probefor specific detection and/or classification into types of a nucleicacid containing said nucleotide sequence, with said oligonucleotidebeing possibly labelled or attached to a solid substrate.

The term “probe” refers to single stranded sequence-specificoligonucleotide which have a sequence which is complementary to thetarget sequence of the HCV genotype(s) to be detected.

Preferably, these probes are about 5 to 50 nucleotides long, morepreferably from about 10 to 25 nucleotides.

The term “solid support” can refer to any substrate to which anoligonucleotide probe can be coupled, provided that it retains itshybridization characteristics and provided that the background level ofhybridization remains low. Usually the solid subtract will be amicrotiter plate, a membrane (e.g. nylon or nitrocellulose) or amicrosphere (bead). Prior to application to the membrane or fixation itmay be convenient to modify the nucleic acid probe in order tofacilitate fixation or improve the hybridization efficiency. Suchmodifications may encompass homopolymer tailing, coupling with differentreactive groups such as aliphatic group, NH₂ groups, SH groups,carboxylic groups, or coupling with biotin or haptens.

The present invention also relates to the use of a composition asdefined above for detecting the presence of one or more HCV genotypes,more particularly for detecting the presence of a nucleic acid of any ofthe HCV genotypes having a nucleotide sequence as defined above, presentin a biologic sample liable to contain them, comprising at least thefollowing steps:

(i) possibly extracting sample nucleic acid,

(ii) possibly amplifying the nucleic acid with at least one of theprimers as defined above or any other HCV subtype 2d, HCV type 3, HCVtype 4, HCV type 5 or universal HCV primer,

(iii) hybrizing the nucleic acids of the biological sample, possiblyunder denatured conditions, and with said nucleic acids being possiblylabelled during or after amplification, at appropriate conditions withone or more probes as defined above, with said probes being preferablyattached to a solid substrate,

(iv) washing at appropriate conditions,

(v) detecting the hybrids formed,

(vi) inferring the presence of one or more HCV genotypes present fromthe observed hybridization pattern,

Preferably, this technique could be performed in the Core or NS5Bregion. The term “nucleic acid” can also be referred to as analyzestrand and corresponds to a single- or double-stranded nucleic acidmolecule. This analyze strand is preferentially positive- or negativestranded RNA, cDNA or amplified cDNA.

The term “biological sample” refers to any biological sample (tissue orfluid) containing HCV nucleic acid sequences and refers moreparticularly to blood serum or plasma samples.

The term “HCV subtype 2d primer” refers to a primer which specificallyamplifies HCV subtype 2d sequences present in a sample (see Examplessection and figures).

The term “HCV type 3 primer” refers to a primer which specificallyamplifies HCV type 3 sequences present in a sample (see Examples sectionand figures).

The term “HCV type 4 primer” refers to a primer which specificallyamplifies HCV type 4 genomes present in a sample.

The term “universal HCV primer” refers to oligonucleotide sequencescomplementary to any of the conserved regions of the HCV genome.

The term “HCV type 5 primer” refers to a primer which specificallyamplifies HCV type 5 genomes present in a sample. The term “universalHCV primer” refers to oligonucleotide sequence complementary to any ofthe conserved regions of the HCV genome.

The expression “appropriate” hybridization and washing condition s areto be as stringent and are generally known in the art (e.g. Maniatis etal., Molecular Cloning: A Laboratory Manual, New York, Cold SpringHarbor Laboratory, 1982).

However, according to the hybridization solution (SSC, SSPE, etc.),these probes should be hybridized at their appropriate temperature inorder to an sufficient specificity.

The term “labelled” refers to the use of labelled nucleic acids. Thismay include the use of labelled nucleotides incorporated during thepolymerase step of the amplification such as illustrate by Saiki et al.(1988) or Bej et al. (1990) or labelled primers, or by any other methodknown to the person skilled in the art.

The process of the invention comprises the steps of contacting any ofthe probes as defined above, with one of the following elements:

either a biological sample in which the nucleic acids are made availablefor hybridiztion,

or the purified nucleic acids contained in the biological sample

or a single copy derived from the purified nucleic acids,

or an amplified copy derived from the purified nucleic acids, with saidelements or with said probes being attached to a solid subsume.

The expression “inferring the presence of one or more HCV genotypespresent from the observed hybridization pattern” refers to theidentification of the presence of HCV genomes in the sample by analyzingthe pattern of binding of a panel of oligonucleotide probes. Singleprobes may provide useful information concerning the presence or absenceof HCV genomes in a sample. On the other hand, the variation of the HCVgenomes is dispersed nature , so rarely is any one probe able toidentify uniquely a specific HCV genome. Rather, the identity of an HCVgenotype may be inferred from the pattern of binding of a panel ofoligonucleotide probes, which are specific for (different) segments ofthe different HCV genomes. Depending on the choice of theseoligonucleotide probes, each known HCV genotype will correspond to aspecific hybridization pattern upon use of a specific combination ofprobes. Each HCV genotype will also be able to be discriminated from anyother HCV genotype amplified with the same primers depending on thechoice of the oligonucleotide probes. Comparison of the generatedpattern of positively hybridizing probes for a sample containing one ormore unkown HCV sequences to a scheme of expected hybridizationpatterns, allows one to clearly infer the HCV genotypes present in saidsample.

The present invention thus relates to a method as defined above, whereinone or more hybridization probes are selected from any of SEQ ID NO 1,3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39,41, 43, 45, 47, 49, 51, 53, 55, 57, 59 or 61, 106, 108, 110, 112, 114,116, 118, 120, 122, 143, 145, 147, 149, 151, 153, 155, 157, 159, 161,163, 165, 167, 169, 171, 173, 175, 177, 179, 181, 183, 185, 187, 198,191, 193, 195, 197, 199, 201, 203, 205, 207, 209, 211, 213, 215, 217,222, 269 or sequence variants thereof, with said sequence variantscontaining deletions and/or insertions of one or more nucleotides,mainly at their extremities (either 3′ or 5′), or substitutions of somenon-essential nucleotides (i.e. nucleotides not essential todiscriminate between genotypes) by others (including modifiednucleotides or inosine), or with said variants consisting of thecomplement of any of the above-mentioned oligonucleotide probes, or withsaid variants consisting of ribonucleotides instead ofdeoxyribonucleotides, all provided that said variant probes can becaused to hybridize with the same specificity as the oligonucleotideprobes from which they are derived.

In order to distinguish the amplified HCV genomes from each other, thetarget polynucleic acids are hybridized to a set of sequence-specificDNA probes targetting HCV genotypic regions located in the HCVpolynucleic acids.

Most of these probes target the most type-specific regions of HCVgenotypes, but some can be caused to hybridize to more than one HCVgenotype.

According to the hybridization solution (SSC, SSPE, etc.), these probesshould be stringently hybridized at their appropriate temperature inorder to attain sufficient specificity. However, by slightly modifyingthe DNA probes, either by adding or deleting one or a few nucleotide attheir extremities (either 3′ or 5′), or substituting some non essentialnucleotides (i.e. nucleotides not essential to discriminate betweentypes) by others (including modified nucleotides or inosine) theseprobes or variants thereof can be caused to hybridize specifically atthe same hybridization conditions (i.e. the same temperature and thesame hybridization solution). Also changing the amount (concentration)of probe used may be beneficial to obtain more specific hybridizationresults. It should be noted in this context, that probes of the samelength, regardless of their GC content, will hybridize specifically atapproximately the same temperature in TMACl solutions (Jacobs et al.,1988).

Suitable assay methods for purposes of the present invention to detecthybrids formed between the oligonucleotide probes and the nucleic acidsequences in a sample may comprise any of the assay formats known in theart, such as the conventional dot-blot format, sandwich hybridizaton orreverse hybridization. For example, the detection can be accomplishedusing a dot blot format the unlabelled amplified sample being bound to amembrane, the membrane being incorporated with at least one labelledprobe meter suitable hybridization and wash conditions, and the presenceof bound probe being monitored.

An alternative and preferred method is a “reverse” dot-blot format, inwhich the amplified sequence contains a label. In this format, theunlabelled oligonucleotide probes are bound to a solid support andexposed to the labelled sample under appropriate stringent hybridizationand subsequent washing conditions. It is to be understood that also anyother assay method which relies on the formation of a hybrid between thenucleic acids of the sample and the oligonucleotide probes according tothe present invention may be used.

According to an advantageous embodiment, the process of detecting one ormore HCV genotypes contained in a biological sample comprises the stepsof contacting amplified HCV nucleic acid copies derived from thebiological sample, with oligonucleotide probes which have beenimmobilized as parallel lines on a solid support.

According to this advantageous method, the probes are immobilized in aLine Probe Assay (LiPA) format. This is a reverse hybridization format(Saiki et al., 1989) using membrane strips onto which severaloligonucleotide probes (including negative or positive controloligonucleotide) can be conveniently applied as parallel lines.

The invention thus also relates to a solid support, preferably amembrane strip, carrying on its surface, one or more probes as definedabove, coupled to the support in the form of parallel lines.

The LiPA is a very rapid and user-friendly hybridization test. Resultscan be read 4 h. after the start of the amplification. Afteramplification during which usually a non-isotopic label is incorporatedin the amplified product, and alkaline denaturation, the amplifiedproduct is contacted with the probes on the membrane and thehybridization is carried out for about 1 to 1.5 h hybridized polynucleicacid is detected. From the hybridization pattern generated, the HCV typecan be deduced either visually, but preferably using dedicated software.The LiPA format is completely compatible with commercially availablescanning devices, thus rendering automatic interpretation of the resultsvery reliable. All those advantages make the LiPA format liable for theuse of HCV detection in a routine setting. The LiPA format should beparticularly advantageous for detecting the presence of different HCVgenotypes.

The present invention also relates to a method for detecting andidentifying novel HCV genotypes, different from the known HCV genomes,comprising the step of:

determining to which HCV genotype the nucleotide present in a biologicalsample belong, according to the process as defied above,

in the case of observing a sample which does not generate ahybridization pattern compatible with those defined in Table 3,sequencing the portion of the HCV genome sequence corresponding to theany hybridizing probe of the new HCV genotype to be determined,

The present invention also relates to the use of a composition asdefined above, for detecting one or more genotypes of HCV present in abiological sample liable to contain them, comprising the steps of:

(i) possibly extracting sample nucleic acid,

(ii) amplifying the nucleic acid with at least one of the primers asdefined above,

(iii) sequencing the amplified products

(iv) inferring the HCV genotypes present from the determine sequences bycomparison to all known HCV sequences.

The present invention also relates to a composition consisting of orcomprising at least one peptide or polypeptide comprising a contiguoussequence of at least 5 amino acids corresponding to a contiguous aminoacid sequence encoded by at least one of the HCV genomic sequences asdefined above, having at least one amino acid differing from thecorresponding region of known HCV (type 1 and/or type 2 and/or type 3)polyprotein sequences as shown in Table 3, or muteins thereof.

It is to be noted that, at the level of the amino acid sequence, anamino acid difference (with respect to known HCV amino acid sequences)is necessary, which means that the polypeptides of the inventioncorrespond to polynucleic acids having a nucleotide difference (withknown HCV polynucleic acid sequences) involving an amino aciddifference.

The new ammo acid sequences, as deduced from the disclosed nucleotidesequences (see SEQ ID NO 1 to 62 and 106 to 123 and 143 to 218, 223 and270), show homologies of only 59.9 to 78% with prototype sequences oftype 1 and 2 for the NS4 region, and of only 53.9 to 68.8% withprototype sequences of type 1 and 2 for the E1 region. As the NS4 regionis known to contain several epitopes, for example characterized inpatent application EP-A-0 489 968, and as the E1 protein is expected tobe subject to immune attack as part of the viral envelope and expectedto contain epitopes, the NS4 and E1 epitopes of the new type 3, 4 and 5isolates will consistency differ from the epitopes present in type 1 and2 isolates. This is examplified by the type-specificity of NS4 syntheticpeptides as presented in example 4, and the type-specificity ofrecombinant E1 proteins in example 11.

After aligning the new subtype 2d type 3, 4 and 5 (see SEQ ID NO 1 to 62and 106 to 123 and 143 to 218, 223 and 270) amino acid sequences withthe prototype sequence of type 1a, 1b, 2a, and 2b, type- andsubtype-specific variable regions can be delineated as presented inFIGS. 5 and 7.

As to the muteins derived from the polypeptides of the invention, Table4 gives an overview of the amino acid substitutions which could be thebasis of some of the muteins as defined above.

The peptides according to the present invention contain preferably atleast 5 contiguous HCV amino acids, preferably however at least 8contiguous amino acids, at least 10 or at least 15 (for instead at least9, 11, 12, 13, 14, 20 or 25 amino acids) of the new HCV sequences of theinvention.

TABLE 4 Amino acids Synonymous groups Ser (S) Ser, Thr, Gly, Asn Arg (R)Arg, His, Lys, Glu, Gln Leu (L) Leu; Ile, Met, Phe, Val, Tyr Pro (P)Pro, Ala, Thr, Gly Thr (T) Thr, Pro, Ser, Ala, Gly, His, Gln Ala (A)Ala, Pro, Gly, Thr Val (V) Val, Met, Ile, Tyr, Phe, Leu, Val Gly (G)Gly, Ala, Thr, Pro, Ser Ile (I) Ile, Met, Len, Phe, Val, Ile, Tyr Phe(F) Phe, Met, Tyr, Ile, Len, Trp, Val Tyr (Y) Tyr, Phe, Trp, Met, Ile,Val, Leu Cys (C) Cys, Ser, Thr, Met His (H) His, Gln, Arg, Lys, Gln, ThrGln (Q) Gln, Glu, His, Lys, Asn, Thr, Arg Asn (N) Asn, Asp, Ser, Gln Lys(K) Lys, Arg, Glu, Gln, His Asp (D) Asp, Asn, Gln, Gln Glu (E) Glu, Gln,Asp, Lys, Asn, His, Arg Met (M) Met, Ile, Len, Phe, Val

The polypeptides of the invention, and particularly the fragments, canbe prepared by classical chemical synthesis.

The synthesis can be carried out in homogeneous solution or in solidphase.

For instance the synthesis technique in homogeneous solution which canbe used is the one described by Houbenweyl in the book entitled “Methodeder organischen chemie” (Method of organic chemistry) edited by E.Wunsh, vol. 15-I et II. THIEME, Stuttgart 1974.

The polypeptides of the invention can also be prepared in solid phaseaccording to the methods described by Atherton and Shepard in their bookentitled “Solid phase peptide synthesis” (IRL Press, Oxford, 1989).

The polypeptides according to this invention can be prepared by means ofrecombinant DNA techniques as described by Maniaitis et al., MolecularCloning: A Library Manual, New York, Cold Spring Harbor Laboratory,1982).

The present invention relates particularly to a polypeptide or peptidecomposition as defined above, wherein said contiguous sequence containsin its sequence at least one of the following amino acid residues: L7,Q43, M44, S60, R67, Q70, T71, A79, A87, N106, K115, A127, A199, S130,V134, G142, I144, E152, A157, V158, P165, S177 or Y177, I178, V180 orE180 or F182, R184, I186, H187, T189, A190, S191 or G191, Q192 or L192or I192 or V192 or E192, N193 or H193 or P193, W194 or Y194, I1195, A197or I197 or V197 or T197, V202, L203 or L203, Q208, A210, V212, F214,T216, R217 or D217 or E217 or V217, H218 or N218, H219 or V219 or L219,L227 or I227, M231 or E231 or Q231, T232 or D232 or A232 or K232, Q235or I1235, A237 or T237, I242, I246, S247, S248, V249, S250 or Y250, I251or V251 or M251 or F251, D252, I254 or V254, L255 or V255, E256 or A256,M258 or F258 or V258, A260 or Q260 or S260, A261, I264 or Y264, M265,I266 or A266, A267, G268 or T268, F271 or M271 or V271, I277, M280 orH280, C284 or A284 or L84, V274, V291, N292 or S292, R293 or I293 orY293, Q294 or R294, L297 or I297 or Q297, A299 or K299 or Q299, N303 orT303, T308 or L308, T310 or F310 or A310 or D310 or V310, L313, G317 orQ317, L333, S351, A358, A359, A363, S364, A366, T369, L373, F376, Q386,I387, S392, 1399, F402, I403, R405, D454, A461, A463, T464, K484, Q500,E501, S521, K522, H524, N528, S531, S532, V534, F536, F537, M539, I546,C1282, A1283, H1310, V1312, Q1321, P1368, V1372, V1373, K1405, Q1406,S1409, A1424, A1429, C1435, S1436, S1456, H1496, A1504, D1510, D1529,I1543, N1567, D1556, N1567, M1572, Q1579, L1581, S1583, F1585, V1595,E1606 or T1606, M1611, V1612 or L1612, P1630, C1636, P1651, T1656 orI1656, L1663, V1667, V1677, A1681, H1685, E1687, G1689, V1695, A1700,Q1704, Y1705, A1713, A1714 or S1714, M1718, D1719, A1721 or T1721,R1722, A1723 or V1723, H1726 or G1726, E1730, V1732, F1735, I1736,S1737, R1738, T1739, G1740, Q1741, K1742, Q1743, A1744, T1745, L1746,E1747 or K1747, L1749, A1750, T1751 or A1751, V1753, N1755, K1756,A1757, P1758, A1759, H1762, T1763, Y1764, P2645, A2647, K2650, K2653 orL2653, S2664, N2673, F2680, K2681, L2686, H2692, Q2695 or L2695 orI2695, V2712, P2715, V2719 or Q2719, T2722, T2724, S2725, R2726, G2729,Y2735, H2739, I2748, G2746 or I2746, I2748, P2752 or K2752, P2754 orT2754, T2757 or P2757,

with said notation being composed of a letter representing the aminoacid residue by its one-letter code, and a number representing the aminoacid numbering according to Kato et al., 1990 as shown in Table 1(comparison with other isolates). See also the numbering in FIGS. 2, 5,7, and 11 (alignment amino acid sequences).

Within the group of unique and new amino acid residues of the presentinvention, the following residues were found to be specific for thefollowing types of HCV according to the HCV classification system usedin the present invention:

Q208, R217, E231, I235, I246, T264, I266, A267, F271, K299, L2686, Q2719which are specific for the HCV subtype 2d sequences of the presentinvention as shown in FIGS. 5 and 2:

Q43, S60, R67, F182, I186, H187, A190, S191, L192, W194, V202, L203,V219, Q231, D232, A237, T254, M280, Q299, T303, L308, and/or L313 whichare specific for the Core/E1 region of HCV type 3 of the invention asshown in FIG. 5;

D1556, Q1579, L1581, S1584, F1585, E1606, V1612, P1630, C1636, T1656,L1663, H1685, E1687, G1689, V1695, Y1705, A1713, A1714, A1721, V1723,H1726, R1738, Q1743, A1744, E1747, I1749, A1751, A1759 and/or H1762which are specific for the NS3/4 region of HCV type 3 sequences of theinvention as shown in FIG. 7;

K2665, D2666, R2670 which are specific for the NS5B region of HCV type 3of the invention as shown in FIG. 2;

L7, A79, A127, S130, E152, V158, I177 or Y177, V180 or E180, R184, T189,Q192 or E192 or 1192, N193 or H193, 1197 or V197, 1203, A210, V212,E217, H218, I4219, L227, A232, V249, I251 or M251, D252, L255 or V255,E256, M258 or V258 or F258, A260 or Q260, M265, T268, V271, V274, M280,I284, N292 or S292, Q294, L297 or I297, T308, A310 or D310 or V310 orT310, and G317 which are specific for the core/E1 region of HCV type 4sequences of the present invention as shown in FIG. 5;

P2645, K2650, P2653, G2656, V2658, I2668, N2673 or N2673, K2681, H2686,D2691, L2692, Q2695 or L2695 or I2695, Y2704, V2712, P715, V2719, I2722,S2725, G2729, Y2735, G2746 or I2746, P2752 or K2752, Q2753, P2754 orT2754, T2757 or P2757 which are specific for the NS5B region of the HCVtype 4 sequences of the present invention as shown in FIG. 2;

M44, Q70, A87, N106, K115, V137, G142, P165, I178, F251, A299, N303,Q317 which are specific for the Core/E1 region of the HCV type 5sequence of the present invention as shown in FIG. 5;

L333, S351, A358, A359, A363, S364, A366, T369, L373, F376, Q386, I387,S392, I399, F102, I403, R405, D454, A461, A463, T464, K484, Q500, E501,S521, K522, H524, N528, S532, V534, F537, M539, I546 which are specificfor the E1/E2 region of the HCV type 5 sequences of the presentinvention as shown in FIG. 12;

C1282, A1283, V1312, Q1321, P1368, V1372, K1405, Q1406, S1409, A1424,A1429, C1435, S1436, S1456, H1496, A1504, D1510, D1529, I1543, N1567,M1572, V1595, T1606, M1611, L1612, I1656, V1667, A1681, A1700, A1713,S1714, M1718, D1719, T1721, R1722, A1723, G1726, F1735, I1736, S1737,T1739, G1740, K1742, T1745, L1746, K1747, A1750, V1753, N1755, A1757,D1758, T1763, and Y1764 which are specific for the NS3/NS4 region of HCVtype 5 sequences of the invention as shown in FIG. 7;

A2647, I2653, S2674, F2680, T2724, R2726, Y2730, H2739 which arespecific for the NS5B region of the HCV type 5 sequences of the presentinvention as shown in FIG. 2;

A256, P1631, V1677, Q1704, E1730, V1732, Q1741 and T1751 which arespecific for the HCV type 3 and 5 sequences of the present invention asshown in FIGS. 5 and 7;

T71, A157, I227, T237, T240, Y250, V251, S260, M271, I2673, T2722, I2748which are specific for the HCV type 3 and 4 sequences of the presentinvention as shown in FIGS. 5 and 2,

V192, Y194, A197, P249, S250, R294 which are specific for the HCV type 4and 5 sequences of the present invention as shown in FIG. 5;

I293 which is specific for the HCV type 4 and subtype 2d sequence of thepresent invention as shown in FIG. 5;

D217 and R294 which are specific for the HCV type 3, 4 and 5 sequencesof the present invention as shown in FIG. 5;

L192 which is specific for the HCV type 3 and subtype 2d sequences ofthe present invention as shown in FIG. 5;

G191 and T197 which are specific for the HCV type 3, 4 and subtype 2dsequences of the preset invention as shown in FIG. 5;

K232 which is specific for the HCV subtype 2d en type 5 sequences of thepresent invention as shown in FIG. 5.

and with said notation being composed of a letter, unambiguouslyrepresenting the amino acid by its one-letter code, and a numberrepresenting the amino acid numbering according to Kato et al., 1990(see also Table 1 for comparison with other isolates), as well as FIG. 2(NS5 region), FIG. 5 (Core/E1 region), FIG. 7 (NS3/NS4 region), FIG. 12(E1/E2 region). Some of the above-mentioned amino acids may be containedin type or subtype Specific epitopes.

For example M231 (detected in type 5) refers to a methionine at position231. A glutamine (Q) is present at the same position 231 in type 3isolates, whereas this position is occupied by an arginine in type 1isolate and by a lysime (K) or asparagine (N) in type 2 isolates (seeFIG. 5).

The peptide or polypeptide according to this embodiment of the inventionmay be possibly labelled, or attached to a solid substrate, or coupledto a carrier molecule such as biotin or mixed with a proper adjuvant.

The variable region in the core protein (V-CORE in FIG. 5) has beenshown to be useful for serotyping (Machida et al., 1992). The sequenceof the disclosed type 5 sequence in this region shows type-specificfeatures. The peptide from amino acid 70 to 78 shows the followingunique sequence for the sequences of the present invention (see FIG. 5):

QPRGRSWGQ (SEQ ID NO 93)

RSEGRTSWAQ (SEQ ID NO 220)

and RTEGRTSWAQ (SEQ ID NO 221)

Another preferred V-Core spanning region is the peptide spanningpositions 60 to 78 of subtype 3c with sequence:

SRRQPIPRARRTEGRSWAQ (SEQ ID NO 268)

Five type-specific variable regions (V to V5) can be identified afteraligning E1 amino acid sequences of the 4 genotypes, as shown in FIG. 5.

Region V1 encompasses amino acids 192 to 203, this is the amino-terminal10 ammo acids of the E1 protein. The following unique sequences as shownin FIG. 5 can be deduced:

LEWRNTSGLYVL (SEQ ID NO 83)

VNYRNASGIYHI (SEQ ID NO 126)

QHYRNISGIYHV (SEQ ID NO 127)

EHYRNASGIYHI (SEQ ID NO 128)

IHYRNASGIYHI (SEQ ID NO 224)

VPYRNASGIYHV (SEQ ID NO 84)

VNYRNASGIYHI (SEQ ID NO 225)

VNYRNASGVYHI (SEQ ID NO 226)

VNYHNTSGIYHL (SEQ ID NO 227)

QHYRNASGIYHV (SEQ ID NO 228)

QHYRNVSGIYHV (SEQ ID NO 229)

IHYRNASDGYYI (SEQ ID NO 230)

LQVKNTSSSYMV (SEQ ID NO 231)

Region V2 encompasses amino acids 213 to 223. The following uniquesequences can be found in the VZ region as shown in FIG. 5:

VYEADDVILHT (SEQ ID NO 85)

VYETEHHILHL (SEQ ID NO 129)

VYEADHHIMHL (SEQ ID NO 130)

VYETDHHILHL (SEQ ID NO 131)

VYEADNLILHA (SEQ ID NO 86)

VWQLRAIVLHV (SEQ ID NO 232)

VYEADYHILHL (SEQ ID NO 233)

VYETDNHILHL (SEQ ID NO 234)

VYETENHILHL (SEQ ID NO 235)

VFETVHHILHL (SEQ ID NO 236)

VFETEHHILHL (SEQ ID NO 237)

VFETDHHIMHL (SEQ ID NO 238)

VYETENHILHL (SEQ ID NO 239)

VYEADALILHA (SEQ ID NO 240)

Region V3 encompasses the amino acids 230 to 242. The following uniqueV3 region sequence can be deduced from FIG. 5:

VQDGNTSTCWTPV (SEQ ID NO 87)

VQDGNTSACWTPV (SEQ ID NO 241)

VRVGNQSRCWVAL (SEQ ID NO 132)

VRTGNTSRCWVPL (SEQ ID NO 133)

VRAGNVSRCWTPV (SEQ ID NO 134)

EEKGNISRCWIPV (SEQ ID NO 242)

VKTGNQSRCWVAL (SEQ ID NO 243)

VRTGNQSRCWVAL (SEQ ID NO 244)

VKTGNQSRCWIAL (SEQ ID NO 245)

VKTGNVSRCWIPL (SEQ ID NO 247)

VKTGNVSRCWISL (SEQ ID NO 248)

VRKDNVSRCWVQI (SEQ ID NO 249)

Region V4 encompasses the amino acids 248 to 257. The following V4region sequences can be deduced from FIG. 5:

VRYVGATTAS (SEQ ID NO 89)

APYIGAPLES (SEQ ID NO 135)

APYVGAPLES (SEQ ID NO 136)

AVSMDAPLES (SEQ ID NO 137)

APSLGAVTAP (SEQ ID NO 90)

APSFGAVTAP (SEQ ID NO 250)

VSQPGALTKG (SEQ ID NO 251)

VKYVGATTAS (SEQ ID NO 252)

APYIGAPVES (SEQ ID NO 253)

AQHLNAPLES (SEQ ID NO 254)

SPYVGAPLEP (SEQ ID NO 255)

SPYAGAPLEP (SEQ ID NO 256)

APYLGAPLEP (SEQ ID NO 257)

APYLGAPLES (SEQ ID NO 258)

APYVGAPLES (SEQ ID NO 259)

VPYLGAPLTS (SEQ ID NO 260)

APHLRAPLSS (SEQ ID NO 261)

APYLGAPLTS (SEQ ID NO 262)

Region V5 encompasses the amino acids 294 to 303. The following uniqueV5 region peptides can be deduced from FIG. 5:

RPRRHQTVQT (SEQ ID NO 91)

QPRRHWTTQD (SEQ ID NO 138)

RPRRHWTTQD (SEQ ID NO 139)

RPRQHATVQN (SEQ ID NO 92)

RPRQHATVQD (SEQ ID NO 263)

SPQHHKFVQD (SEQ ID NO 264)

RPRRLWTTQE (SEQ ID NO 265)

PPRIHETTQD (SEQ ID NO 266)

The variable region in the E2 region (HVR-2) of type 5a as shown in FIG.12 spanning amino acid positions 471 to 484 is also a preferred peptideaccording to the present invention with the following sequence:

TISYANGSGPSDDK (SEQ ID NO 267)

The above given list of peptides are particularly suitable for vaccineand diagnostic development.

Also comprised in the present invention is any synthetic peptide orpolypeptide containing at least 5 contiguous amino acids derived fromthe above-defined peptides in their peptidic chain.

According to a specific embodiment, the present invention relates to acomposition as defined above, wherein said contiguous sequence isselected from any of the following HCV amino acid type 3 sequences:

a sequence having a homology of more than 72%, preferably more than 74%,more preferably more than 77% and most preferably more than 80 or 84%homology to any of the amino acid sequences as represented in SEQ ID NO14, 16, 18, 20, 22, 24, 26 or 28 (HD10, BR36, BR33 sequences) in theregion spanning positions 140 to 319 in the Core/E1 region as shown inFIG. 5:

a sequence having a homology of more than 70%, preferably more than 72%,more preferably more than 75% homology, most preferably more than 81%homology to any of the amino acid sequences as represented in SEQ ID NO14, 16, 18, 20, 22, 24, 26 or 28 (HD10, BR36, BR33 sequences) in the E1region spanning positions 192 to 319 as shown in FIG. 5;

a sequence having a homology of more than 86%, preferably more thy 88%,and most preferably more than 90% homology to the amino acid sequencesas representd in SEQ ID NO 148 (type 3c); BE98 in the region spanningpositions 1 to 110 in the Core region as shown in FIG. 5;

a sequence having a homology of more than 76%, preferably more than 78%,most preferably more than 80% to any of the amino acid sequences asrepresented in SEQ ID NO 30, 32, 34, 36, 38 or 40 (HCC153, HD10, Br36sequences) in the region spanning positions 1646 to 1764 in the NS3/NS4region as shown in FIGS. 7 and 11;

a sequence having a homology of more than 81%, preferably more than 83%,and most preferably more than 86% homology to any of the amino acidsequences as represented in SEQ ID NO 14, 16, 18, 20, 22, 24, 26 or 28(HD10, BR36, BR33 sequences) in the region spanning positions 140 to 319in the Core/E1 region as shown in FIG. 5;

a sequence having a homology of more than 81.5%, preferably more than83%, and most preferably more than 86% homology to any of the amino acidsequences as represented in SEQ ID NO 14, 16, 18, 20. 22, 24, 26 or 28(HD10, BR36, BR33 sequences) in the E1 region spanning positions 192 to319 as shown in FIG. 5;

a sequence having a homology of more than 86%, preferably more than 88%,and most preferably more than 90% to the amino acid sequence asrepresented in SEQ ID NO 150; (type 3c BE98) in the region spanningpositions 2645 to 2757 in the NS5B region as shown in FIG. 2.

According to yet another embodiment, the present invention relates to acomposition as defined above, wherein said contiguous sequence isselected from any of the following HCV amino acid type 4 sequences:

a sequence having a homology of more than 80%, preferably more than 82%,most preferably more than 84% homology to any of the amino acidsequences as represented in SEQ ID NO 119, 121, and 123 (GB358, GB549,GB809 sequences) in the region spanning positions 127 to 319 of theCore/E1 region as shown in FIG. 5;

a sequence having a homology of more than 80%, preferably more than 82%,most preferably more than 84% homology to any of the amino acidsequences as represented in SEQ ID NO 119, 121, and 123 (GB358, GB549,GB809 sequences) in the region spanning positions 127 to 319 of theCore/E1 region as shown in FIG. 5;

a sequence having a homology of more than 73%, preferably more than 75%,most preferably more than 78% homology in the E1 region spanningpositions 192 to 319 to any of the amino acid sequences as representedin SEQ ID NO 119, 121, and 123 (GB358, GB549, GB809 sequences) in theregion spanning positions 140 to 319 of the Core/E1 region as shown inFIG. 5;

a sequence having more than 85%, preferably more than 86%, mostpreferably more than 87% homology to any of the amino acid sequences asrepresented in SEQ ID NO 19, 121, or 123 (GB358, GB549, GB809 sequences)in the region spanning positions 192 to 319 of E1 as shown in FIG. 5;

a sequence showing more than 73%, preferably more than 74%, mostpreferably more than 75% homology to any of the amino acid sequences asrepresented in SEQ ID NO 107, 109, 111, 113, 115 or 117 (GB48, GB116,GB215, GB358, GB549, GB809 sequences) in the region spanning positions2645 to 2757 of the NS5B region as shown in FIG. 2;

a sequence having any of the sequences as represented in SEQ ID NO 164or 166 (GB809 and CAM600 sequences) in the Core region as shown in FIG.5;

a sequence having any of the sequences as represented in SEQ ID NO 168,170, 172, 174, 176, 178, 180, 182, 184, 186, 188 or 190 (CAM600, GB809,CAMG22, CAMG27, GB549, GB438, CAR4/1205, CAR4/901, GB116, GB215, GB958,GB809-4 sequences) in the Core/E1 region as shown in FIG. 5;

a sequence having any of the sequences as represented in SEQ ID NO 194,196, 148, 200, 202, 204, 206, 208, 210, 212 (GB358, GB724, BE100, PC,CAM600, CAMG22, etc.) in the NS5B region or in SEQ ID NOs: 198, 200 inthe NS3/4 region.

The above-mentioned type 4 peptides polypeptides comprise at least anamino acid sequence selected from any HCV type 4 polyprotein with theexception of core sequence as disclosed by Simmonds et al. (1993, EG-29,see FIG. 5).

According to yet another aspect, the present invention relates to acomposition as defined above, wherein said contiguous sequence isselected from any of the following HCV amino acid type 5 sequences:

a sequence having more than 93%, preferably more than 94%, mostpreferably more than 95% homology in the region spanning Core positions1 to 191to any of the amino acid sequences as represented in SEQ ID NO42, 44, 46, 48, 50, 52 or 54 (PC sequences) and SEQ ID NO 152 (BE95) asshown in FIG. 5;

a sequence having more than 73%, preferably more than 74%, mostpreferably more than 76% homology in the region spanning E1 positions192 to 319 to any of the amino acid sequences as represented in SEQ IDNO 42, 44, 46, 48, 50, 52 or 54 (PC sequences) as shown in FIG. 5;

a sequence having a more than 78%, preferably more than 80%, mostpreferably more than 83% homology to any of the amino acid sequences asrepresented in SEQ ID NO 42, 44, 46, 48, 50, 52, 54, 154, 156 (BE95,BE100) (PC sequences) in the region spanning positions 1 to 319 of theCore/E1 region as shown in FIG. 5;

a sequence having more than 90%, preferably more than 91%, mostpreferably more than 92% homology to any of the amino acid sequencesrepresented in SEQ ID NO 56 or 58 (PC sequences) in the region spanningpositions 1286 to 1403 of the NS3 region as shown in FIGS. 7 or 11;

a sequence having more than 66%, more particularly 68%, mostparticularly 70% or more homology to any of the amino acid sequences asrepresented in SEQ ID NO 60 or 62 (PC sequences) in the region spanningpositions 1646 to 1764 of the NS3/4 region as shown in FIGS. 7 or 11.

According to yet another embodiment, the present invention relates to acomposition as defined above, wherein said contiguous sequence isselected from any of the following HCV amino acid type 2d sequences:

a sequence having more than 83%, preferably more than 85%, mostpreferably more than 87% homology to the amino acid sequence asrepresented in SEQ ID NO 144 (NE92) in the region spanning positions 1to 319 of the Cor/E1 region as shown in FIG. 5;

a sequence having more than 79%, preferably more than 81%, mostpreferably more than 84% homology in the region spanning E1 positions192 to 319 to the amino acid sequence as represented in SEQ ID NO 144(NE92) as shown in FIG. 12;

a sequence having more than 95%, more particularly 96%, mostparticularly 97% or more homology to the amino acid sequence asrepresented in SEQ ID NO 146 (NE92) in the region spanning positions2645 to 2757 of the NS5B region as shown in FIG. 2.

The present invention also relates to a recombinant vector, particularlyfor cloning and/or expression, with said recombinant vector comprising avector sequence, an appropriate prokaryotic, eukaryotic or viralpromoter sequence followed by the nucleotide sequences as defined above,with said recombinant vector allowing the expression of any one of theHCV type 2 and/or HCV type 3 and/or type 4 and/Dr type 5 derivedpolypeptides as defied above in a prokaryotic, or eukaryotic host or inliving mammals when injected as naked DNA, and more particularly arecombinant vector allowing the expression of any of the following HCVtype 2d, type 3, type 4 or type 5 polypeptides spanning the followingamino acid positions:

a polypeptide starting at position 1 and ending at any position in theregion between positions 70 and 326, more particularly a polypeptidespanning positions 1 to 70, 1 to 85, positions 1 to 120, positions 1 to150, positions 1 to 191, positions 1 to 200, for expression of the Coreprotein, and a polypeptide spanning positions 1 to 263, positions 1 to326, for expression of the Core and E1 protein;

a polypeptide starting at any position in the region between positions117 and 192, and ending at any position in the region between positions263 and 326, for expression of E1, or forms that have the putativemembrane anchor deleted (positions 264 to 293 plus or minus 8 aminoacids);

a polypeptide starting at any position in the region between positions1556 and 1688, and ending at any position in the region betweenpositions 1739 and 1764, for expression of the NS4 regions, moreparticularly a polypeptide starting at position 1658 and ending atposition 1711 for expression of the NS4a antigen, and more particularly,a polypeptide starting at position 1712 and ending between positions1743 and 1972, for example 1712-1743, 1712-1764, 1712-1782, 1712-1972,1712 to 1782 and 1902 to 1972 for expression of the NS4b protein orparts thereof.

The term “vectors” may comprise a plasmid, a cosmid, a phage, or avirus.

In order to carry out the expression of the polypeptide of the inventionin bacteria such as E. coli or in eukaryotic cells such as in S.cerevisiae, or in cultured vertebrate or invertebrate hosts such asinsect cells. We Hamster Ovary (CHO), COS, BHK, and MDCK cells, thefollowing steps are carried out:

transformation of an appropriate cellular host with a recombinantvector, in which a nucleotide sequence coding for one of thepolypeptides of the invention has been inserted under the control of theappropriated regulatory elements, particularly a promoter recognized bythe polymerases of the cellular host and, in the case of a prokaryotichost, an appropriate ribosome binding site (RBS), enabling theexpression in said cellular host of said nucleotide sequence. In thecase of an eukaryotic host any artificial signal sequence or pre/prosequence might be provided, or the natural HCV signal sequence might beemployed, e.g. for expression of E1 the signal sequence starting betweenamino acid positions 117 and 170 and ending at amino acid position 191can be used, for expression of NS4, the signal sequence starting betweenamino acid positions 1646 and 1659 can be used,

culture of said transformed cellular host-under conditions enabling theexpression of said insert.

The present invention also relates to a composition as defined above,wherein said polypeptide is a recombinant polypeptide expressed by meansof an expression vector as defied above.

The present invention also relates to a composition as defined above,for use in a method for immunizing a mammal, preferably humans, againstHCV comprising administering a sufficient amount of the compositionpossibly accompanied by pharmaceutically acceptable adjuvants, toproduce an immune response, more particularly a vaccine compositionincluding HCV type 3 polypeptides derived from the Core, E1 or the NS4region and/or HCV type 4 and/or HCV type 5 polypeptides and/or HCV type2d polypeptides.

The present invention also relates to an antibody raised uponimmunization with a composition as defined above by means of a processas defined above, with said antibody being reactive with any of thepolypeptides as defined above, and with said antibody being preferably amonoclonal antibody.

The monoclonal antibodies of the invention can be produced by anyhybridoma liable to be formed according to classical methods fromsplenic cells of an animal, particularly from a mouse or rat, immunizedagainst the HCV polypeptides according to the invention, or muteinsthereof, or fragments thereof as defined above on the one hand, and ofcells of a myeloma cell line on the other hand, and to be selected bythe ability of the hybridoma to produce the monoclonal antibodiesrecognizing the polypeptides which has been initially used for theimmunization of the animals.

The antibodies involved in the invention can be labelled by anappropriate label of the enzymatic, fluorescent, or radioactive type.

The monoclonal antibodies according to this preferred embodiment of theinvention may be humanized versions of mouse monoclonal antibodies madeby means of recombine DNA technology, departing from parts of mouseand/or human genomic DNA sequences coding for H and L chains or fromcDNA clones coding for H and L chains.

Alternatively the monoclonal antibodies according to this preferredembodiment of the invention may be human monoclonal antibodies. Theseantibodies according to the present embodiment of the invention can alsobe derived from human peripheral blood lymphocytes of patients infectedwith type 3, type 4 or type 5 HCV, or vaccinated against HCV. Such humanmonoclonal antibodies are prepared, for instance, by means of humanperipheral blood lymphocytes (PBL) repopulation of severe combinedimmune deficiency (SCID) mice (for recent review, see Duchosal et al.1992).

The invention also relates to the use of the proteins of the invention,muteins thereof, or peptides derived therefrom for the selection ofrecombinant antibody by the process of repertoire cloning (Persson etal., 1991).

Antibodies directed to peptides derived from a certain genotype may beused either for the detection of such HCV genotypes, or as therapeuticagents.

The present invention also relates to the use of a composition asdefined above for incorporation into an immunoassy for detecting HCV,present in biological sample liable to contain it, comprising at leastthe following steps:

(i) contacting the biological sample to be analyzed for the presence ofHCV antibodies with any of the compositions as defined above preferablyin an immobilized form under appropriate conditions which allow theformation of an immune complex, wherein said polypeptide can be abiotinyl polypeptide which is covalently bound to a solid substrate bymeans of streptavidin or avidin complexes,

(ii) removing unbound components,

(iii) incubating the immune complexes formed with heterologousantibodies, which specifically bind to the antibodies present in thesample to be analyzed, with said heterologous antibodies havingconjugated to a detectable label under appropriate conditions,

(iv) detecting the presence of said inmmunecomplexes visually or bymeans of densitometry and inferring the HCV serotype present from theobserved hybridization pattern

The present invention also relates to the use of a composition asdefined above, for incorporation into a serotyping assay for detectingone or more serological types of HCV present in a biological sampleliable to contain it, more particularly for detecting E1 and NS4antigens or antibodies of the different types to be detected combined inone assay format, comprising at least the following steps:

(i) contacting the biological sample to be analyzed for the presence ofHCV antibodies or antigens of one or more serological types, with atleast one of the compositions as defined above, an immobilized formunder appropriate conditions which allow the formation of animmunecomplex,

(ii) removing unbound components,

(iii) incubating the immunecomplexes formed with heterologousantibodies, which specifically bind to the antibodies present in thesample to be analyzed, with said heterologous antibodies havingconjugated to a detectable label under appropriate conditions,

(iv) detecting the presence of said immunecomplexes visually or by meansof densitometry and interring the presence of one or more HCVserological types present from the observed binding pattern.

The present invention also relates to the use of a composition asdefined above, for immobilization on a solid substrate and incorporationinto a reversed phase hybridization assay, preferably for immobilizationas parallel lines onto a solid support such as a membrane strip, fordetermining the presence or the genotype of HCV according to a method asdefied above.

The present invention thus also relates to a kit for determining thepresence of HCV genotypes as defined above present in a biologicalsample liable to contain them, comprising:

possibly at least one primer composition containing any primer selectedfrom those defined above or any other HCV type 3 and/or HCV type 4,and/or HCV type 5, or universal HCV primers,

at least one probe composition as defined above, with said probes beingpreferentially immobilize on a solid substrate, and more preferentiallyon one and the same membrane strip,

a buffer or components necessary for producing the buffer enablinghybridiztion reaction between these probes and the possibly amplifiedproducts to be carried out,

means for detecting the hybrids resulting from the precedinghybriziation,

possibly also including an automated scanning and interpretation devicefor inferring the HCV genotypes present in the sample from the observedhybridization pattern.

The genotype may also be detected by means of a type-specific antibodyas defined above, which is linked to any polynucleic sequence that canafterwards be amplified by PCR to detect the immune complex formed(Immuno-PCR, Sano et al., 1992);

The present invention also relates to a kit for determining the presenceof HCV antibodies as defined above present in a biological sample liableto contain them, comprising:

at least one polypeptide composition as defined above, preferentially incombination with other polypeptides or peptides from HCV type 1, HCVtype 2 or other types of HCV, with said polypeptides beingpreferentially immobilized on a solid substrate, and more preferentiallyon one and the same membrane strip,

a buffer or components necessary for producing the buffer enablingbinding reaction between these polypeptides and the antibodies againstHCV present in the biological sample,

means for detecting the immunecomplexes formed in the preceding bindingreaction,

possibly also including an automated scanning and interpretation devicefor inferring tie HCV genotypes present in the sample from the observedbinding pattern.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1

Alignment of consensus nucleotide sequences for each of the type 3aisolates BR34, BR36, and BR33, deduced from the clones with SEQ ID NO 1,5, 9; type 4 isolates GB48, GBB 116, GB215, GB358, GB549, GB809, CAM600,CAMG22, G1438, CAR4/1205, CAR1/501 (SEQ ID NO. 106, 108, 110, 112, 114,116, 201, 203, 205, 207, 209 and 211); type 5a isolates BE95 and BE96(SEQ ID NO 159 and 161) and type 2d isolate NE92 (SEQ ID NO 145) fromthe region between nucleotides 7932 and 8271, with known sequences fromthe corresponding region of isolates HCV-1, HCV-J, HC-J6, HC-J8, T1 andT9, and others as shown in Table 3.

FIG. 2

Alignment of amino acids sequences deduce from the nucleic acidsequences as represented in FIG. 1 from the subtype 3a clones BR34 (SEQID NO 2, 4), BR36 (SEQ ID NO 6, 8) and BR33 (SEQ ID NO 10, 12), thesubtype 3c clone BE98 (SEQ ID NO 150), and the type 4 clones GB48 (SEQID NO 10f7), GB116 (SEQ ID NO 109), GB215 (SEQ ID NO 111), GB358 (SEQ IDNO 113), GB549 (SEQ ID NO 115) GB809 (SEQ ID NO 117); CAM600, CAMG22,GB438, CAR4/1205, CAR1/501 (SEQ ID NO 202, 204, 206, 208, 210, 212): thetype 5a clones BE95 and BE96 (SEQ ID NO 160 and 162); as well as thesubtype 2d isolate NE92 (SEQ ID NO 146) from the region between aminoacids 2645 to 2757 with known sequences from die corresponding region ofisolates HCV-1, HCV-J, HC-J6, and HC-J8, T1 and T9, and other sequencesas shown in Table 3.

FIG. 3

Alignment of type 2d, 3c, 4 and 5a nucleotide sequences from isolatesNE92, BE98, GB358, GB809, CAM600, GB3724, BE95 (SEQ ID NO 143, 147, 191,163, 165, 193 and 151) in the Core region between nucleotide positions 1and 500, with known sequences from the corresponding region of type 1,type 2, type 3 and type 4 sequences.

FIG. 4

Alignment of nucleotide sequences for the subtype 2d isolate NE92 (SEQID NO 143), the type 4 isolates GB358 (SEQ ID NO 118 and 187), GB549(SEQ ID NO 120 and 175), and GB809-2 (SEQ ID NO 122 and 169), GB 809-4,BG116, GB215, CAM600, CAMG22, CAMG27, GB438, CAR4/1205, CAR4/901 (SEQ IDNO 189, 183, 185, 167, 171, 173, 177, 179, 181), sequences for each ofde subtype 3a isolates HD10, 8R36, and BR33, (SEQ ID NO 13, 15, 17(HD10), 19, 21 (BR36) and 23, 25 or 27 (BR23) and the subtype 5aisolates BE95 and BE100(SEQ ID NO 143 and 195) from the region betweennucleotide 379 and 957, with known sequences from the correspondingregion of type 1 and 2 and 3.

FIG. 5

Alignment of amino acid sequences from the new HCV nucleotide sequencesof the Core/E1 region of isolates BR33, BR36, HD10, GB358, GB549, andGB809, PC or BE95, CAM600, and GB724 (SEQ ID NO. 14, 20, 24, 119 or 192,121, 123 or 164, 54 or 152, 166 and 194) from the region betweenpositions 1 and 319, with known sequences from type 1a (HCV-1), type 1b(HCV-J), type 2a (HC-JG), type 2b (RC-J8), NZL1, RCV-TR, positions 7-89of type 3a (E-b1), and positions 8-88 of type 4a (EG-29). V-Core,variable region with type-specific features in the core protein, V1,variable region 1 of the E1 protein, V2, variable region 2 of the E1protein, V3, variable region 3 of the E1 protein, V4, variable region 4of the E1 protein, V5, variable region 5 of the E1 protein.

FIG. 6

Alignment of nucleotide sequences of isolates HCl53, HD10 and BR36,deduced from clones with SEQ ID NO 29, 31, 33, 35, 37 and 39, from dieNS314 region between nucleotides 4664 to 5292, with known sequences fromthe corresponding region of isolates HCV-1, HCV-J, HC-J6, and HC-J8,EB1, EB2, EB6 and EB7.

FIG. 7

Alignment of amino acid sequences deduced from the new HCV nucleotidesequences of the NS3/NS4 region of isolate BR36 (SEQ ID NO 36, 38 and40) and BE95 (SEQ ID NO 270). NS4-1, indicates the region that wassynthesized as synthetic peptide 1 of the NS4 region, NS4-5, indicatesthe region that was synthesized as synthetic peptide 5 of the NS4region; NS4-7, indicates the region that was synthesized as syntheticpeptide 7 of the NS4 region.

FIG. 8

Reactivity of the LIPA-selected (Stuyver et al., 1993) type 3 sera onthe Inno-LIA HCV Ab II assay (Imnogenetics) (left), and on the NS4LIAtest For the NS4-LIA test, NSA-1, NS4-5, and NS4-7 peptides weresynthesized based on the type 1 (HCV-1), type 2 (HC-J6) and type 3(BR36) prototype isolate sequences as shown in Table 4, and applied asparallel lines onto a membrane strip as indicated, 1, serum BR33, 2,serum HD10, 3, serum DKH.

FIG. 9

Nucleotide sequences of Core/E1 clones obtained from the PCR fragmentPC-2, PC-3, and PC-4, obtained from serum BE95 (PC-2-1 (SEQ ID NO 41),PC-2-6 (SEQ ID NO 43), PC-4 -1 (SEQ ID NO 45), PC-4-6 (SEQ ID NO 47),PC-3-4 (SEQ ID NO 49), and PC-3-8 (SEQ ID NO 51)) of subtype Sa isolateBE95.

A consensus sequence is shown for die Core and E1 region of isolateBE95, presented as PC C/E1 with SEQ ID NO 53, Y, C or T, R, A or G, S, Cor G.

FIG. 10

Alignment of nucleotide sequences of clones with SEQ ID NO 197 and 199(PC sequences, see also SEQ ID NO 55, 57, 59) and SEQ ID NO 35, 37 and39 (BR36 sequences) from the NS3/4 region between nucleotides 3856 to5292, with known sequences from the corresponding region of isolatesHCV-1, HCV-1, HC-J6, and HC-J8.

FIG. 11

Alignment of amino acid sequences of subtype 5a BE95 isolate PC cloneswith SEQ ID NO 56 and 58, from the NS3/4 region between amino acids 1286to 1764, with known sequences from the corresponding region of isolatesHCV-1, HCV-J, HC-J6, and HC-J8.

FIG. 12

Alignment of amino acid sequences of subtype 5a isolate BE9S (SEQ ID NO158) in the E1/E2 region spanning positions 328 to 546, with insequences from the corresponding region of isolates HCV-1, HCV-J, HC-J6,HC-J8, NZL1 and HCV-TR (see Table 3).

FIG. 13

Alignment of the nucleotide sequences of subtype 5a isolate BE95 (SEQ IDNO 157) in the E1/E2 region with known HCV sequences as shown in Table3.

EXAMPLE Example 1 The NS5b Region of HCV Type 3

Type 3 sera, selected by means of the INNO-LiPA HCV research kit(Stuyver et al., 1993) from a number of Brazilian blood donors, werepositive in the HCV antibody ELISA (Innotest HCV Ab II; Innogenetics)and/or in the INNO-LIA HCV Ab n confirmation test (Innogenetics). Onlythose sera that were positve after the first round of PCR reactions(Stuyver et al., 1993) were retained to further study.

Reverse transcription and nested PCR: RNA was extracted from 50 μl serumand subjected to cDNA synthesis as described (Stuyver et al., 1993).This cDNA was used as template for PCR, for which the total volume wasincreased to 50 μl containing 10 pmoles of each primer, 3 μl of 10× Pfubuffer 2 (Stratagene) and 2.5 U of Pfu DNA polymerase (Stratagene). ThecDNA was amplified aver 45 cycles consisting of 1 mn 94° C., 1 min 50°C. and 2 min 72° C. The amplified products were separated byelectrophoresis, isolated, cloned and sequenced as described (Stuyver etal., 1993).

Type 3a and 3b-specific primers in the NS5 region were selected from thepublished sequences (Mori et al., 1992) as follows:

for type 3a:

HCPr161(+): 5′-ACCGGAGGCCAGGAGAGTGATCTCCTCC-3′ (SEQ ID NO 63) and

HCPr162(−): 5′-GGGCTGCTCTATCCTCATCGACGCCATC-3′ (SEQ ID NO 64);

for type 3b:

HCPr163(+): 5′-GCCAGAGGCTCGGAAGGCGATCAGCGCT-3′ (SEQ ID NO 65) and

HCPr164(−): 5′-GAGCTGCTCTGTCCTCCTCGACGCCGCA-3′ (SEQ ID NO 66)

Using the Line Probe Assay (LiPA) (Stuyver et al., 1993), sevenhigh-titer type 3 sera were selected and subsequently analyzed with theprimer sets HCPr161/162 for type 3a, and HCPr163/164 for type 3b. Noneof these sera was positive with the type 3b primers. NS5 PCR fragmentsobtained using the type 3a primers from serum BR36 (BR36-23), serum BR33(BR33-2) and serum BR34 (BR34-4) were selected for cloning. Thefollowing sequences were obtained from the PCR fragments:

From fragment BR34-4:

BR34-4-20 (SEQ ID NO 1), BR34-4-19 (SEQ ID NO 3)

From fragment BR36-23;

BR36-23-18 (SEQ ID NO 5), BR36-23-20 (SEQ ID NO 7)

From fragment BR33-2:

BR33-2-17 (SEQ ID NO 9), BR33-2-21 (SEQ ID NO 11)

An alignment of sequences with SEQ ID NO 1, 5 and 9 with known sequencesis given in FIG. 1. An alignment of the deduced amino acid sequences isshown in FIG. 2. The 3 isolates are very closely related to each other(mutual homologies of about 95%) and to the published sequences of type3a (Mori et al., 1992), but are only distantly related to type 1 andtype 2 sequences (Table 5). Therefore, it is clearly demonstrated thatNS5 sequences from LiPA-selected type 3 sera are indeed derived from atype 3 genome. Moreover, by analyzing the NS5 region of serum BR34, forwhich no 5′UR sequences were determined as described in Stuyver et al.(1993), the excellent correlation between typing by means of the LiPAand genotyping as deduced from nucleotide sequencing was further proven.

Example 2 The Core/E1 Region of HCV Type 3

After aligning the sequences of HCV-1 (Choo et al., 1991). HCV-J (Katoet al., 1990), HC-J6 (Okamoto et al., 1991), and HC-J8 (Okamoto et al.,1992), PCR primers were chosen in those regions of little sequencevariation. Primers HCPr23(+): 5′-CTCATGGGGTACATTCCGCT-3′ (SEQ ID NO 67)and HCP54(−): 5′-TATTACCAGTTCATCATCATATCCCA-3′ (SEQ ID NO 68), weresynthesized on a 392 DNA/RNA synthesizer (Applied Biosystems). This setof primers was selected to amplify the sequence from nucleotide 397 to957 encoding amino acids 140 to 319 (Kato et al., 1990): 52 amino acidsfrom the carboxyterminus of core and 128 amino acids of E1 (Kato et al.,1990). The amplification products BR36-9, BRR33-1, and HD10-2 werecloned as described (Stuyver et al., 1993). The following clones wereobtained from the PCR fragments:

From fragment HD10-2:

HD10-2-5 (SEQ ID NO 13), HD10-2-14 (SEQ ID NO 15), HD10-2-21 (SEQ ID NO17)

From fragment BR36-9:

BR36-9-13 (SEQ ID NO 19), BR36-9-20 (SEQ ID NO 21).

From fragment BR33-1:

BR33-1-10 (SEQ ID NO 23), BR33-1-19 (SEQ ID NO 25), BR33-1-20 (SEQ ID NO27).

An alignment of the type 3 E1 nucleotide sequences (HD10, BR36, BR33)with SEQ ID NO 13, 19 and 23 with known E1 sequences is presented inFIG. 4. Four variations were detected in the E1 clones from serum HD10and BR36, while only 2 were found in BR33. All are silent third lettervariations, with the exception of mutations at position 40 (L to P) and125 (M to I). The homologies of the type 3 E1 region (without core) withtype 1 and 2 prototype sequences are depicted in Table 5.

In total, 8 clones covering the core/E1 region of 3 different isolateswere sequenced and the E1 portion was compared with the known genotypes(Table 3) as shown in FIG. 5. After computer analysis of the deducedamino acid sequence, a signal-anchor sequence at the core carboxyterminus was detected which might, through analogy with type 1b(Hijikata et al., 1991), promote cleavage before the LEWRN sequence(position 192, FIG. 5; SEQ ID NO:271). The L-to-P mutation in one of theHD10-2 clones resides in this signal-anchor region and potentiallyimpairs recognition by signal peptidase (computer prediction). Since noexamples of such substitutions were found at this position in previouslydescribed sequences, this mutation might have resulted from reversetranscriptase or Pfu polymerase misincorporation. The 4 amino-terminalpotential N-linked glycosylation sites, which are also present in HCVtypes la and 2, remain conserved in type 3. The N-glycosylation site intype 1b (aa 250, Kato et al., 1990) remains a unique feature of thissubtype. All E1 cysteines, and the putative transmembrane region (aa 264to 293, computer prediction) containing the aspartic acid at position279, are conserved in all three HCV types. The following hypervariableregions can be delineated: V1 from aa 192 to 203 (numbering according toKato et al., 1990), V2 (213-223), V3 (230-242), V4 (248-257and V5(294-303). Such hydrophilic regions are thought to be exposed to thehost defense mechanisms. This variability might therefore have beeninduced by the host's immune response. Additional putative N-linkedglycosylation sites in the V4 region in all type 1b isolates known todayand in the V5 region of HC-J8 (type 2b) possibly further contribute tomodulation of the immune response. Therefore, analysis of this region,in the present invention, for type 3 and 4 sequences has beeninstrumental in the delineation of epitopes that reside in the V-regionsof E1, which will be critical for future vaccine and diagnosticsdevelopment.

Example 3 The NS3/NS4 Region of HCV Type 3

For the NS3/NS4 border region, the following sets of primers wereselected in the regions of little sequence variability after aligningthe sequences of HCV-1 (Choo et al., 1991), HCV-J (Kato et al.,1990),HC-J6 (Okamoto et al., 1991), and HC-J8 (Okamoto et al., 1992) (smallercase lettering is used for nucleotides added for cloning purposes):

set A:

HCPr116(+): 5′-ttttAAATACATCATGRCITGYATG-3′ (SEQ ID NO 69)

HCPr66 (−): 5′-ctattaTTGTATCCCRCTGATGAARTCCACAT-3′ (SEQ ID NO 70)

set B:

HCPr116(+): 5′-ttttAAATACATCATGRCTTGYATG-3′ (SEQ ID NO 69)

HCPr118(−): 5′-actagtcgactaYTGIATICCRCTIATRWARTTCCACAT-3 ′ (SEQ ID NO71)

set C:

HCPr117(+): 5′-ttttAAATACATCGCIRCITGCATGCA-3′ (SEQ ID NO 72)

HCPr66 (−): 5′-ctattaTTGTATCCCRCTGATGAARTCCACAT-3′ (SEQ ID NO 70)

set D:

HCPr117(+): 5′-ttttATACATCGCIRCITGCATGCA-3′ (SEQ ID NO 72)

HCPr118(−): 5′-actagtcgactaYTGIATICCRCTIATRWARTTCCACAT-3′ (SEQ ID NO 71)

set E:

HCPr116(+): 5′-tttAAATACATCATGRCITGYATG-3′ (SEQ ID NO 69)

HCPr119(−): actagtcgactaRTTIGCGCIATIAGCCGTRTTCCAYTG-3′ (SEQ ID NO 73)

set F:

HCPr117(+): 5′-ttttATACATCGCIRCITGCATGCA-3′ (SEQ ID NO 72)

HCPr119(−): actagtcgactaRTTIGCIATIAGCCGTRTTCATCCAYTG-3′ (SEQ ID NO 73)

set G:

HCPr131 (+): 5′-ggaattctagaCCITCITGGGAYGARAYITGGAARTG-3′ (SEQ ID NO 74)

HCPr66 (−): 5′-cattaTTGTATCCCRCTGATGAARTTCCACAT-3′ (SEQ ID NO 70)

set H:

HCPr130(+): 5′-ggaattctagACIGCITAYCARGCIACIGTITGYGC-3′ (SEQ ID NO 75)

HCPr66 (−): 5′-ctattaTTGTATCCCRCTGATGAARTCCACAT-3′ (SEQ ID NO 70)

set I:

HCPr134(+): 5′-CATATAGATGCCCACTTATC-3′ (SEQ ID NO 76)

HCPr66 (−): 5′-ctattaTTGTATCCCRCTGATGAARTTCCACAT-3′ (SEQ ID NO 70)

set J:

HCPr131(+): 5′-ggaattctagaCCITCITGGGAYGARAYITGGAARTG-3′ (SEQ ED NO 74)

HCPr118(−): 5′-actagtcgactaYTGIATICCRCTIATRWARTTCCACAT-3′ (SEQ ID NO 71)

set K:

HCPr130(+): 5′-ggaattctagACIGCITAYCARGCIACIGTITGYGC-3′ (SEQ ID NO 75)

HCPr118(−): 5′-actagtcgactaYTGIATICCRCTIATRWARTTCCACAT-3′ (SEQ ID NO 71)

set L:

HCPr134(+): 5′-CATATAGATGCCCACTTCCTATC-3′ (SEQ ID NO 76)

HCPr118(−): 5′-actatcgactaYTGIATICCRCTIATRWARTTCCACAT-3(SEQ ID NO71)

set M:

HCPr3(+): 5′-GTGTGCCAGGACCATC-3′ (SEQ ID NO 77) and

HCPr4(−): 5′-GACATGCATGTCATGATGTA-3 (SEQ ID NO 78)

set N:

HCPr3(+): 5′-GTGCCAGGACCATC-3′ (SEQ ID NO 77 and

HCPr118(−): 5′-actagtcgactaYTGIATICCRCTIATRWARTTCCACAT-3′ (SEQ ID NO 71)

set O:

HCPr3(+): 5′-GTGTGCCAGGACCATC-3′ (SEQ ID NO 77) and

HCPr66 (−): 5′-ctattaTTGTATCCCRCGATGAARTTCCACAT-3′ (SEQ ID NO 70)

No PCR products could be obtained with the sets of primers A, B, C, D,E, F, G, H, I, J, K, L, M, and N, on random-primed cDNA obtained fromtype 3 sera With the primer set O, no fragment could be amplified fromtype 3 sera. However, a smear containing a few weakly stainable bandswas obtained from serum BR36. After sequence analysis of several DNAfragments, purified and cloned from the area around 300 bp on theagarose gel, only one clone, HCC153 (SEQ ID NO 29), was shown to containHCV information. This sequence was used to design primer HCPr152.

A new primer set P was subsequently tested on several sera.

set P:

HCPr152(+): 5′-TACGCCTCTTCATATCGGTGGGGCCTG-3′ (SEQ ID NO 79) and

HCPr66(−): 5′-CTATTATGTATCCCRCTGATGAARTTCCACAT-3′ (SEQ ID NO 70)

The 464-bp HCPr152/66 fragment was obtained from serum BR36 (BR3620) andserum HD10 (HD10-1). The following clones were obtained from these PCRproducts:

From fragment HD10-1:

HD10-1-25 (SEQ ID NO 31), HD10-1-3 (SEQ ID NO 33),

From fragment BLR36-20:

BR36-20-164 (SEQ ID NO 35), BR36-20-165 (SEQ ID NO 37), BR36-20-166 (SEQID NO 39).

The nucleotide sequences obtained from clones with SEQ ID NO 29, 31, 33,35, 37 or 39 are shown aligned with the sequences of prototype isolatesof other type of HCV in FIG. 6. In addition to one silent 3rd lettervariation, one 2nd letter mutation resulted in an E to G substitution atposition 175 of the deduced amino acid sequence of BR36 (FIG. 7). SerumHD10 clones were completely identical. The two type 3 isolates werenearly 94% homologous in this NS4 region. The homologies with othertypes are presented in Table 5.

Example 4 Analysis of the Anti-NS4 Response to Type-specific Peptides

As the NS4 sequence contains the information for an important epitopecluster, and since antibodies towards this region seem to exhibit littlecross-reactivity (Chan et al., 1991), it was worthwhile to investigatethe type-specific antibody response to this region. For each of the 3genotypes, HCV-1 (Choo et al., 1991), HC-J6 (Okamoto et al., 1991) andBR36 (present invention), three 20-mer peptides were synthesizedcovering the epitope region between acids 1688 and 1743 (as depicted intable 6). The synthetic peptides were applied as parallel lines ontomembrane strips. Detection of anti-NS4 antibodies and color developmentwas performed according to the procedure described for the INNO-LIA HCVAb II kit (Innogenetics, Antwerp). Peptide synthesis was carried out ona 9050 PepSynthesizer (Millipore). After incubation with 15LiPA-selected type 3 sera, 9 samples showed reactivity towards NS4peptides of at least 2 different types, but a clearly positive reactionwas observed for 3 sera (serum BR33, RD30 and DKH) on the type 3peptides, while negative (serum BR33 and HD30) or indeterminate (serumDKH) on the type 1 and type 2 NS4 peptides; 3 sera tested negative foranti-NS4 antibodies (FIG. 8). Using the same membrane strips coated withthe 9 peptides as indicated above and as shown in FIG. 8, 38 type 1 sera(10 type 1a and 28 type 1b), 11 type 2 sera (10 type 2a and 1 type 2b),12 type 3a 2 type 4 sera (as determined by the LiPA procedure) were alsotested. As shown in Table 8, the sera reacted in a genotype-specificmanner with the NS4 epitopes. These results demonstrate thattype-specific anti-NS4 antibodies can be detected in the sera of somepatients. Such genotype-specific synthetic peptides might be employed todevelop serotyping assays, for example a mixture of the nine peptides asindicated above, or combined with the NS4 peptides from the HCV type 4or 6 genotype or from new genotypes corresponding to the region betweenamino acids 1688 and 1743, or synthetic peptides of the NS4 regionbetween amino acids 1688 and 1743 of at least one of the 6 genotypes,combined with the E1 protein or deletion mutants thereof, or syntheticE1 peptides of at least one of the genotypes. Such compositions could befurther extended with type-specific peptides or proteins, including forexample the region between amino acids 68 and 91 of the core protein, ormore preferably the region between amino acids 68 and 78. Furthermore,such type-specific antigens may be advantageously used to improvecurrent diagnostic screening and confirmation assays and/or HCVvaccines.

Example 5 The Core and E1 Regions of HCV Type 5

Sample BE95 was selected from a group of sera that reacted positive in aprototype Line Probe Assay as described earlier (Stuyver et al., 1993),because a high-titer of HCV RNA could be detected, enabling cloning offragments by a single round of PCR. As no sequences from any codingregion of type 5 has been disclosed yet, synthetic oligonucleotide forPCR amplification were chosen in the regions of little sequencevariation after aligning the sequences of HCV-1 (Choo et al., 1991),HCV-J (Kato et al., 1990), HC-J6 (Okamoto et al., 1991), HC-J8 (Okamotoet al., 1992), and the new type 3 sequences of the present inventionHD10, BR33, and BR36 (see FIG. 5, Example 2). The following sets ofprimers were synthesized on a 392 DNA/RNA synthesizer (AppliedBiosystems):

Set 1:

HCPr52(+): 5′-atgTTGGGTAAGGTCATCGATACCCT-3′ (SEQ ID NO 80) and

HCPr54(−): 5′-ctattaCCAGTTCATCATCATATCCCA-3′ (SEQ ID NO 78)

Set 2:

HCPr41(+): 5′-CCCGGGAGGTCTCGTAGACCGTGCA-3′ (SEQ ID NO 81) and

HCPr40(−): 5′-ctattaAAGATAGAGAAAGAGCAACCGGG-3′ (SEQ ID NO 82)

Set 3:

HCPr41(+): 5′-CCCGGGAGGTCTCGTAGACCGTGCA-3′ (SEQ ID NO 81) and

HCPr54(−): 5′-ccattaCCAGTTCATCATCATATCCCA-3′ (SEQ ID NO 78)

The three sets of primers were employed to amplify the regions of thetype 5 isolate PC as described (Stuyver et al., 1993). Set 1 was used toamplify the E1 region and yielded fragment PC-4, set 2 was designed toyield the Core region and yielded fragment PC-2. Set 3 was used toamplify the Core and E1 region and yielded fragment PC-3. Thesefragments were cloned as described (Stuyver et al., 1993). The followingclones were obtained from the PCR fragments:

From fragment PC-2:

PC-2-1 (SEQ ID NO 41), PC-2-6 (SEQ ID NO 43),

From fragment PC-4:

PC4-1 (SEQ ID NO 45), PC-4-6 (SEQ ID NO 47),

From fragment PC-3:

PC-3-4 (SEQ ID NO 49), PC-3-8 (SEQ ID NO 51)

An alignment of sequences with SEQ ID NO 41, 43, 45, 47, 49 and 51, isgiven in FIG. 9. A consensus amino acid sequence (PC C/E1 ; SEQ ID NO54) can be deduced from each of the 2 clones cloned from each of thethree PCR fragments as depicted in FIG. 5, which overlaps the regionbetween nucleotides 1 and 957 (Kato et al., 1990). The 6 clones are veryclosely related to each other (mutual homologies of about 99.7%).

An alignment of nucleotide sequence with SEQ ID NO 53 or 151 (PC C/E1from isolate BE95) with known nucleotide sequences from the Core/E1region is given in FIG. 3. The clone is only distantly related to type1, type 2, type 3 and type 4 sequences (Table 5).

Example 6 NS3/NS4 Region of HCV Type 5

Attempts were undertaken to clone the NS3/NS4 region of the isolateBE95, described in example 5. The following sets of primers wereselected in the regions of little sequence variability after aligningthe sequences of HCV-1 (Choo et al., 1991), HCV-J (Kato et al., 1991),HC-J6 (Okamoto et al., 1991), and HC-J8 (Okamoto et al., 1992) and ofthe sequences obtained from type 3 sera of the present invention (SEQ IDNO 31, 33, 35, 37 and 39); smaller case lettering is used fornucleotides added for cloning purposes:

set A:

HCPr116(+): 5′-ttttAAATACATCATGRCITGYATG-3′ (SEQ ID NO 66)

HCPr66 (−): 5′-ctattaTTGTATCCCRCTGATGAARTTCCACAT-3′ (SEQ ID NO 70)

set B;

HCPr116(+): 5′-ttttAAATACATCATGRCITGYATG-3′ (SEQ ID NO 69)

HCPr118(−): 5′-actagtcgactaYTGIATICCRTIATRWARTTCCACAT-3′ (SEQ ID NO71)

set C:

HCPr117(+): 5′-ttttAAATACATCGCIRCITGCATGCA-3′ (SEQ ID NO 72)

HCPr66 (−): 5′-ctatta-TTGTATCCCRCTGATGAARTTCCACAT-3′ (SEQ ID NO 70)

set D:

HCPr117(+): 5′-ttttAAATACATCGCIRCITGCATGCA-3′ (SEQ ID NO 72)

HCPr118(−): 5′-actagtcgactaYTGIATICCRCTIATRWARTCCACAT-3′ (SEQ ID NO 71)

set E:

HCPr116(+): 5′-ttttAAATACATCATGRCITGYATG-3′ (SEQ ID NO 69)

HCPr119(−): actagtcgactaRTTCIATIAGCCG/TRTTCATCCAYTG-3′ (SEQ ID NO 73)

set F:

HCPr117(+): 5′-ttttAAATACATCGCIRCITGCATGCA-3′ (SEQ ID NO 72)

HCPr119(−): actagtcgactaRTTIGCIATIAGCCG/TRTTCATCCAYTG-3′ (SEQ ID NO 73)

set G:

HCPr131(+): 5′-ggaattctagaCCITCITGGGAYGARAYITGGAARTG-3′ (SEQ ID NO 74)

HCPr66 (−): 5′-ctattaTTGTATCCCRCTGATGAARTTCCACAT-3′ (SEQ ID NO 70)

set H:

HCPr130(+): 5′-ggaattctagCIGCITAYCARGCIACIGTTGYGC-3′ (SEQ ID NO 75)

HCPr66 (−): 5′-ctattaTTGTATCCCRCTGATGAARTTCCACAT-3′ (SEQ ID NO 70)

set I:

HCPr134(+): 5′-CATATAGATGCCCACTTCCTATC-3′ (SEQ ID NO 76)

HCPr66 (−): 5′-ctattaTTGTATCCCRCTGATGAARTTCCACAT-3′ (SEQ ID NO 70)

set J:

HCPr131(+): 5′-ggaattctagaCCITCITGGGAYGARAYITGGAARTG-3′ (SEQ ID NO 74)

HCPr118(−): 5′-actagtcgactaYTGIATICCRCTIATRWARTTCCACAT-3′ (SEQ ID NO 71)

set K:

HCPr130(+): 5′-ggaarttctagACIGCITAYCARGCIACIGTITGYGC-3′ (SEQ ID NO 75)

HCPr118(−): 5′-actagtcgactaYTGIATICCRCTIATRWARTTCCACAT-3′ (SEQ ID NO 71)

set L:

HCPr134(+): 5′-CATATAGATGCCCACTTCCTATC-3′ (SEQ ID NO 76)

HCPr118(−): 5′-actgtcgactaYTGIATICCRCTIATRWARTTCCACAT-3′ (SEQ ID NO 71)

set M:

HCPr3(+): 5′-GTTGCCAGGACCATC-3′ (SEQ ID NO 77) and

HCPr4(−): 5′-GACATGCATGTCATGATGTA-3′ (SEQ ID NO 78)

set N:

HCPr3(+): 5′-GTGTGCCAGGACCATC-3′ (SEQ ID NO 77) and

HCPr 118(−): 5-acagtcgactaYTGIATICCRCTIATRWARTFCCACAT-3′ (SEQ ID NO 71)

set O:

HCPr3(+): 5′-GTGTGCCAGGACCATC-3′ (SEQ ID NO 77) and

HCPr66 (−): 5′-ctattaTTGTATCCCRCTGATGAARTTCCACAT-3′ (SEQ ID NO 70)

No PCR products could be obtained with the sets of primers A, B, C, D,E, F, G, H, I, J, K, L, M, and N, on random-primed cDNA obtained fromtype 3 sera. However, set O yielded what appeared to be a PCR artifactfragment estimated about 1450 base pairs, instead of the expected 628base pairs. Although it is not expected that PCR artifact fragmentscontain information of the gene or genome that was targetted in theexperiment, efforts were put in cloning of this artifact fragment, whichwas designated fragment PC-1.

The following clones, were obtained from fragment PC-1:

PC-1-37 (SEQ ID NO 59 and SEQ ID NO 55), PC-1-48 (SEQ ID NO 61 and SEQID NO 57)

The sequences obtained from the 5′ and 3′ ends of the clone are given inSEQ ID NOS 55, 57, 59, and 61, and the complete sequences with SEQ ID NO197 and 199 are shown aligned with the sequences of prototype isolatesof other types of HCV in FIG. 10 and the alignment of the deduced aminoacid sequences is shown in FIG. 11 and 7. Surprisingly, the PCR artifactclone contained HCV information. The positions of the sequences withinthe HCV genome are compatible with a contiguous HCV sequence of 1437nucleotides, which was the estimated size of the cloned PCR artifactfragment. Primer HCPr66 primed correctly at the expected position in theHCV genome. Therefore, primer HCPr3 must have incidentally misprimed ata position 809 nucleotides upstream of its legitimate position in theHCV genome. This could not be expected since no sequence information wasavailable from a coding region of type 5.

Example 7 The E2 Region of HCV Type 5

Serum BE95 was chosen for experiments aimed at amplifying a part of theE2 region of HCV type 5.

After aligning the sequences of HCV-1 (2), HCV-J(1), HC-J6 (3), andHC-J8 (4), PCR primers were chosen in those regions of little sequencevariation.

Primers HCPr109(+): 5′-TGGGATATGATGATGAACTGGTC-3′ (SEQ ID NO 141) andHCPr14(−): 5′-CCAGGTACAACCGAACCAATTGCC-3′ (SEQ ID NO 142) were combinedto amplify the aminoterminal region of the E2/NS1 region, and weresynthesized on a 392 DNA/RNA synthesizer (Applied Biosystems). Withprimers HCPr109 and HCPr14, a PCR fragment of 661 bp was generated,containing 169 nucleotides corresponding to the E1 carboxyterminus and492 bases from the region encoding the E2 aminoterminus.

An alignment of the type 5 E1/E2 sequences with seq ID NO. 158 withknown sequences is presented in FIG. 10. The deduced protein sequencewas compared with the different genotypes (FIG. 12, amino acids328-546). In the E1 region, there were no extra structural importantmotifs found. The aminoterminal of E2 was hypervariable when comparedwith the other genotypes. All 6 N-glycosylation sites and all 7 cysteineresidue's were conserved in this E2 region. To preserve alignment, itwas necessary to introduce a gap between aa 474 and 475 as for type 3a,but not between aa 480 and 481, as for type 2.

Example 8 The NS5b Region of HCV Type 4

Type 4 sera GB48, GB116, GB215, and GB358, selected by means of the lineprobe assay (LiPA, Stuyver et al., 1993), as well as sera GB549 andGB809 that could not be typed by means of this LiPA (only hybridizationwas observed with the universal probes), were selected from Gabonesepatients. All these sera were positive after the first round of PCRreactions for the 5 untranslated region (Stuyver et al., 1993) and wereretained for further study.

RNA was isolated from the sera and cDNA synthesized as described inexample 1.

Universal primers in the NS5 region were selected a alignment of thepublished sequences as follows:

HCPr206(+): 5′-TGGGGATCCCGTATGATACCCGCTGCITGA-3′ (SEQ ID NO. 124) and

HCPr207(−): 5′-GGCGGAATCCTGTCATAGCCTCCGTGAA-3′ (SEQ ID NO. 125);

and were synthesized on a 392 DNA/RNA synthesizer (Applied Biosystems).Using the Line Probe Assay (LiPA), four high-titer type 4 sera and 2sera that could not be classified were selected and subsequentlyanalysed with the primer set HCPr206/207. NS5 PCR fragments obtainedusing these primers from serum GB48 (GB48-3), serum GB 116 (GB 116-3),serum GB215 (GB215-3), serum GB358 (GB358-3), serum GB549 (GB549-3), andserum GB809 (GB809-3), were selected for cloning. The followingsequences were obtained from the PCR fragments:

From fragment G48-3: GB48-3-10 (SEQ ID NO. 106)

From fragment GB116-3: GB116-3-5 (SEQ ID NO. 108)

From fragment GB215-3: GB215-3-8 (SEQ ID NO. 110)

From fragment GB358-3: GB358-3-3 (SEQ ID NO. 112)

From fragment GB549-3: GB549-3-6 (SEQ ID NO. 114)

From fragment GB809-3: GB809-3-1 (SEQ ID NO. 116)

An alignment of nucleotide sequences with SEQ ID NO. 106, 108, 110, 112,114, and 116 with known sequences is given in FIG. 1. An alignment ofdeduced amino acid sequences with SEQ ID NO. 107, 109, 111, 113, 115,and 117with known sequences is given in FIG. 2. The 4 isolates that hadbeen typed as type 4 by means of LiPA arm very closely related to eachother (mutual homologies of about 95%), but are only distantly relatedto type 1, type 2, and type 3 sequences (e.g. GB358 shows homologies of65.6 to 67.7% with other genotypes, Table 4). The sequence obtained fromsera GB549 and GB809 also show similar homologies with genotypes 1, 2,and 3 (65.9 to 68.9% for GB549 and 65.0 to 68.5% for GB809, Table 4),but an intermediate homology of 79.7 to 86.8% (often observed betweensubtypes of the same type) exists between GB549 or GB509 with the groupof isolates consisting of GB48, GB116, GB215, and GB358, or betweenGB549 and GB809. These data indicate the discovery of 3 new subtypeswithin the HCV genotype 4: in the present invention, these 3 subtypesare designated subtype 4c, represented by isolates GB48, GB 116, GB215,and GB358, subtype 4g, represented by isolate GB549, and subtype 4e,represented by isolate GB809. Although the homologies observed betweensubtypes in the NS5 region seem to indicate a closer relationshipbetween subtypes 4c and 4e, the homologies observed in the E1 regionindicate that subtypes 4g and 4e show the closest reason (see example8).

Example 9 The Core/E1 Region of HCV Type 4

From each of the 3 new type 4 subtypes, one representative serum wasselected for cloning experiments in the Core/E1 region. GB549 (subtype4g) and GB809 (subtype 4e) were anayzed together with isolate GB358 thatwas chosen from the subtype 4c group. Synthetic oligonucleotide:

After aligning the sequences of HCV-1 (2), HCV-J(1), HC-J6 (3), andHC-J8 (4), PCR primers were chosen in those regions of little sequencevariation.

Primers HCPr52(+): 5′-atgTTGGGTMGGTCATCGATACCCT-3′ (SEQ ID NO:80),HCPr23(+): 5′-CTCATGGGGTACATTCCGCT-3′ (SEQ ID NO:67), and HCPr54(−):5′-CTATTACCAGTTCATCATCATATCCCA-3′ (SEQ ID NO:68), were synthesized on a392 DNA/RNA synthesizer (Applied Biosystems). The sets of primersHCPr23/54 and HCPr52/54 were used, but only with the primer setHCPr52/54, PCR fragments could be obtained. This set of primersamplified the sequence from nucleotide 379 to 957 encoding amino acids127 to 319: 65 amino acids from the carboxyterminus of core and 128amino acids of E1. The amplification products GB358-4, GB549-4, andGB804-4 were cloned as described in example 1. The following wereobtained from PCR fragments:

From fragment GB358-4: GB358-4-1 (SEQ ED NO 118)

From fragment GB549-4: GB549-4-3 (SEQ ID NO 120)

From fragment GB809-4: GB809-4-3 (SEQ ID NO 122)

An alignment of the type 4 Core/E1 nucleotide sequences with seq ID NO.118, 120, and 122 with Known sequences is presented in FIG. 4. Thehomologies of the type 4 E1 region (without core) with type 1, type 2,type 3, and type 5 prototype sequences are depicted in Table 4.Homologies of 53 to 66% are observed with representative isolates ofnon-type 4 genotypes. Observed homologies in the E1 region within type4, between the different subtypes, ranges from 75.2 to 78.4%. Therecently disclosed sequences of the care region of Egyptian type 4isolates (for example EG-29 in FIG. 3) described by Simmonds et al.(1993) do not allow alignment with the Gabonese sequences (as describedin the present invention) in the NSB region and may belong to differenttype 4 subtypes(s) as can be deduced from the core sequences. Thededuced amino acid sequences with SEQ ID NO 119, 121, and 123 arealigned with other prototype sequences in FIG. 5. Again, type-specificvariation mainly resides in the variable V regions, designated in thepresent invention, and therefore, type-4-specific amino acids or Vregions will be instrumental in diagnosis and therapeutics for HCV type4.

Example 10 The Core/E1 and NS5 b Regions of new HCV Type 2, 3 and 4Subtype

Samples NE92(subtype 2d), BE98 (subtype 3c), CAM600 and GB809 (subtype4e), CAMG22 and CAMG27 (subtype 4f), GB438 (subtype 4h), CAR4J1205subtype (4i), CAR1/501 (subtype 4j), CAR1/901 (subtype 4?), and GB724(subtype 4?) were selected from a group of sera that reacted positivebut aberrantly in a prototype Line Probe Assay as described earlier(Stuyver et al., 1993). Another type 5a isolate BE100was also analyzedin the C/E1 region, and yet another type 5a isolate BE96 in the NS5bregion. A high-titer of HCV RNA could be detected, enabling cloning offragments by a single round of PCR. As no sequences from any codingregion of these subtypes had been disclosed yet, syntheticoligonucleotide for PCR amplification were chosen in the regions oflittle sequence variation after aligning the sequences of HCV-1 (Choo etal., 1991), HCV-1 (Kato et al., 1990). HC-J6 (Okamoto et al., 1991).HC-J8 (Okamoto et al., 1992), and the other new sequences of the presentinvention.

The above mentioned sets 1, 2 and 3 (see example 5) of primers were usedbut only with set 1, PCR fragments could be obtained from all isolates(except for BE98. GB724, and CAR1/501). This set of primers amplifiedthe sequence from nucleotide 379 to 957 encoding amino acids 127 to 319:65 amino acids from the carboxyterminus of core and 128 amino acids ofE1. With set 3, the core/E1 region from isolate NE92 and BE98 could beamplified, and with set 2, the core region of GB358, GB724, GB809, andCAM600 could be amplified. The amplification products were cloned asdescribed in example 1. The following clones were obtained from the PCRfragments:

From isolate GB724, the clone with SEQ ID NO 193 from the core region.

From isolate NE92, the clone with SEQ ID NO 143

From isolate BE98, the clone from the core/E1 region of which part ofthe sequence has been analyzed and is given in SEQ ID NO 147,

From isolate CAM600, the clone with SEQ ID NO 167 from the E1 region, orSEQ ID NO 165 from the Core/E1 region as shown in FIG. 3,

From isolate CAMG22, the clone with SEQ ID NO 171 from the E1 region asshown in FIG. 4,

from isolate GB358, the clone with SEQ ID NO 191 in the core region,

from isolate CAMG27, the clone with SEQ ID NO 173 from the core/E1region,

from isolate GB438, the clone with SEQ ID NO 177 from the core/ E1region,

from isolate CRA4/1205, the clone with SEQ ID NO 179 from the core/E1region,

from isolate CAR1/901, the clone with SEQ ID NO 181 from the core/E1region,

from isolate GB809, the clone GB809-4 with SEQ ID NO 189 from thecore/E1 region,

clone GB809-2 with SEQ ID NO 169 from the core/E1 region and the clonewith SEQ ID NO 163 from the core region, and from isolate BE100, theclone with SEQ ID NO 155 from the Core/E1 region as shown in FIG. 4.

An alignment of these Core/E1 sequences with known Core/E1 sequences ispresented in FIG. 4. The deduced amino acid sequences with SEQ ID NO144, 148, 164, 168, 170, 172, 174, 178, 180, 182, 190, 192, 194, 156,166 are aligned with other prototype sequences in FIG. 5. Again,type-specific variation mainly resides in the variable V regions,designated in the present invention, and therefore, type 2d, 3c and type4-specific amino acids or V regions will be instrumental in diagnosisand therapeutics for HCV type (subtype) 2d, 3c or the different type 4subtypes.

The NS5 b region of isolates NE92, BE98, CAM600, CAMG22, GB438,CAR4/1205, CAR1/501, and BE96 was amplified with primers HCPr206 andHCPr207 (Table 7). The corresponding clones were cloned and sequenced asin example 1 and the corresponding sequences (of which BE98 was partlysequenced) received the following identification numbers.

NE92: SEQ ID NO 145

BE98: SEQ ID NO 149

CAM600: SEQ ID NO 201

CAMG22: SEQ ID NO 203

GB438: SEQ ID NO 207

CAR4/1205: SEQ ID NO 209

CAR1/501: SEQ ID NO 211

BE95: SEQ ID NO 159

BE96: SEQ ID NO 161

An alignment of these NS5b sequences with know NS5b sequences ispresented in FIG. 1. The deduced amino acid sequences with SEQ ID NO146, 150, 202, 204, 206, 208, 210, 212, 160, 162 are alignment withother prototype sequences in FIG. 2. Again, subtype-specific variationscan be observed, and therefore, type 2d, 3c and type 4-specific aminoacids or V regions will be instrumental in diagnosis and therapeuticsfor HCV type (subtype) 2d, 3c or the different type 4 subtypes.

Example 11 Genotype-specific Reactivity of Anti-E1 Antibodies(Serotyping)

E1 proteins were expressed from vanccinia virus constructs containing acore/E1 region extending from nucleotide positions 355 to 978 (Core/E1clones described in previous examples including the primers HCPr52 andHCPr54), and expressed proteins from L119 (after the initiatormethionine) to W326 of the HCV polyprotein. The expressed protein wasmodified upon expression in the appropriate host cells (e.g. HeLa, RK13,HuTK-, HepG2) by cleavage between amino acids 191 and 192 of the HCVpolyprotein and by the addition of high-mannose type carbohydratemotifs. Therefore, a 30 to 32 kDa glycoprotein could be observed onwestern blot by means of detection with serum from patients withhepatitis C.

As a reference, a genotype 1b clone obtained form the isolate HCV-B wasalso expressed in an identical way as described above, and was expressedfrom recombinant vaccinia virus vvHCV-11A.

A panel of 104 genotyped sera was first tested for reactivity with acell lysate containing type 1b protein expressed from the recombinantvaccinia virus vvHCV-11A, and compared with cell lysate of RK13 cellsinfected with a wild type vaccinia virus (‘E1/WT’). The lysates werecoated as a 1/20 dilution on a normal ELISA microtiter plate (Nuncmaxisorb) and left to react with a 1120 diluation of the respectivesera. The panel consisted of 14 type 1a, 38 type 1b, 21 type 2, 21 type3a, and 9 type 4 sera. Human antibodies ware subsequently detected by agoat anti-human IgG conjugated with peroxidase and the enzyme activitywas detected. The optical density values of the E1 and wild type lysateswere divided and a factor 2 was taken as the cut-off. The results aregiving in the table A. Eleven out of 14 type 1a sera (79%), 25 out of 38type 1b sera (66%), 6 out of 21 (29%), 5 out of 21 (24%), and none ofthe 9 type 4 or the type 5 serum reacted (0%). These experiments clearlyshow the high prevalence of anti-E1 antibodies reactive with the type 1E1 protein in patients infected with type 1(36/52 (69%)) (either type 1aor type 1b), but the low prevalence or absence in non-type 1sera (11/52(21%)).

TABLE A serum E1/WT type 1a 3748 3.15 3807 3.51 5282 1.99 9321 3.12 93242.76 9325 6.12 9326 10.56 9356 1.79 9388 3.5 8366 10.72 8380 2.27 109254.02 10936 5.04 10938 1.36 type 1b 5205 2.25 5222 1.33 5246 1.24 525013.58 5493 0.87 5573 1.75 8243 1.77 8244 2.05 8316 1.21 8358 5.04 933714.47 9410 5 9413 5.51 10905 1.26 10919 5.00 10928 8.72 10929 8.26 109312.3 10932 4.41 44 2.37 45 3.14 46 4.37 47 5.68 48 2.97 49 1.18 50 9.8551 4.51 52 1.11 53 5.20 54 0.98 55 1.48 56 1.06 57 3.85 58 7.6 59 3.2860 3.23 61 7.82 62 1.92 type 2 23 0.91 24 1.16 25 2.51 26 0.96 27 1.2028 0.96 29 2.58 30 8.05 31 0.92 32 0.82 33 5.75 34 0.79 35 0.86 36 0.8537 0.76 38 0.92 39 1.08 40 2.33 41 2.83 42 1.21 43 0.91 type 3 1 6.88 21.47 3 3.06 4 6.52 5 10.24 6 2.72 7 1.11 8 1.54 9 1.60 10 1.21 11 1.0712 1.00 13 0.85 14 0.96 15 0.51 16 1.00 17 1.09 18 0.99 19 1.04 20 1.0421 0.96 type 4 22 0.87 GB48 0.49 GB113 0.68 GB116 0.73 GB215 0.52 GB3580.56 GB359 0.71 GB438 1.08 GB516 1.04 type 5 BE95 0.86

Core/E1 clones of isolates BR36 (type 3a) and BE95 (type 5a) weresubsequently recombined into the viruses vvHCV-62 and vvHCV-63,respectively. A genotyped panel of sera was subsequently tested ontocell lysates obtained from RK13 cells infected with the recombinantviruses vvHCV-62 and vvHCV-63. Tests were carried out as described aboveand the results are given in the table given below (TABLE B). From theserests, it can clearly be seen that, although some cross-reactivityoccurs (especially between type 1 and 3), the obtained values of a givenserum are usually higher on its homologous E1 protein than on an E1protein of another genotype. For type 5 sera, none of the 5 sera werereactive on type 1 or 3 E1 proteins, while 3 out of 5 were shown tocontain anti-E1 antibodies when tested on their homologous type 5protein. Therefore, in this simple test system, a considerable number ofsera can already be serotyped. Combined with the reactivity totype-specific NS4 epitopes or epitopes derived from other type-specificparts of the HCV polyprotein, a serotyping assay may be developed fordiscriminating the major types of HCV. To overcome the problem ofcross-reactivity, the position of cross-reactive epitopes may bedetermined by someone skilled in the art (e.g. by means of competitionof the reactivity with synthetic peptides), and the epitopes evokingcross-reactivity may be left out of the composition to be included inthe serotyping assay or may be included in sample diluent to outcompetecross-reactive antibodies.

TABLE B serum E1^(1b)/WT E1^(3a)/WT E1^(5a)/WT type 1b 8316 0.89 0.590.80 8358 2.22 2.65 1.96 9337 1.59 0.96 0.93 9410 16.32 9.60 3.62 94139.89 2.91 2.85 10905 1.04 0.96 1.05 10919 3.17 2.56 2.96 10928 4.39 2.282.07 10929 2.95 2.07 2.08 10931 3.11 1.49 2.11 5 0.86 0.86 0.96 6 3.481.32 1.32 7 6.76 4.00 3.77 8 10.88 3.44 4.04 9 1.76 1.88 1.58 10 9.887.48 7.20 11 8.48 8.99 8.45 12 0.76 0.72 0.76 13 5.04 5.67 5.37 14 10.4810.54 11.22 15 5.18 1.62 1.65 type 3 8332 3.39 4.22 0.66 10907 3.24 4.390.96 10908 0.99 0.94 0.98 10934 0.86 0.90 0.90 10927 2.58 2.71 2.44 82100.82 0.80 0.86 8344 1.09 6.66 1.17 8351 1.21 1.29 1.22 30 0.85 4.11 0.9832 0.85 2.16 1.04 type 5 0.78 0.95 1.54 BE110 0.79 1.01 4.95 BE95 0.470.52 0.65 BE111 0.71 0.75 8.33 BE112 1.01 1.27 2.37 BE113 1.11 1.35 1.60

TABLE 5 Homologies of new HCV sequences with other known HCV typesRegion Isolate 1a 1b 2a 2b 3a 3b (nucleotides) (type) HCV-1 HCV-J HC-J6HC-J8 T1 T7 T9 T10 Core (1-573)   PC (5)  83.8 (91.6) 84.8 (92.1) 82.6(90.1) 82.4 (89.0) E1 (574-957)  HD10 (3)  61.5 (68.0) 64.6 (68.8) 57.8(55.5) 56.3 (59.4) BR36 (3) 62.0 (66.4) 62.5 (67.2) 56.5 (53.9) 55.2(58.6) BR33 (3) 60.7 (67.2) 63.3 (68.0) 56.5 (54.7) 56.0 (58.6)   PC(5)  61.4 (64.0) 62.4 (64.8) 54.1 (49.6) 53.3 (47.2)  GB358 (4a)  62.5(69.1) 62.8 (65.9) 59.4 (54.0) 54.4 (54.0)  GB549 (4b)  66.0 (72.2) 62.8(69.8) 59.1 (56.4) 56.5 (54.0)  GB809 (4c)  63.3 (69.1) 60.7 (64.3) 56.7(53.2) 53.0 (51.6) NS3   PC (5)  74.7 (89)   76.1 (86.4) 76.1 (89.8)78.0 (89.0) (3856-4209) NS4 BR36 (3) 67.8 (78.5) 69.8 (75.1) 62.0 (67.5)61.7 (66.0) (4892-5292)  HD10 (3)  69.8 (74.6) 66.6 (69.7) 57.8 (59.9)59.1 (59.9) NS4   PC (5)  61.3 (62.2) 63.0 (65.5) 52.9 (46.2) 54.3(43.7) (4936-5292) NS5b BR34 (3) 65.7     66.7     63.9     64.3    94.8 93.9 75.6 77.0 (8023-8235) BR36 (3) 64.3     67.6     64.8    66.7     94.8 93.4 75.1 76.5 BR33 (3) 65.7     67.1     64.3    64.8     94.8 93.9 76.0 77.5  GB358 (4a)  67.7 (76.1) 65.6 (77.0) 66.5(70.8) 65.6 (71.7)  GB549 (4b)  68.8 (76.1) 67.1 (77.0) 65.9 (71.7) 65.9(74.4)  GB809 (4c)  68.5 (73.5) 65.0 (73.5) 67.7 (69.9) 67.7 (73.5)Shown are the nucleotide homologies (the amino-acid homology is givenbetween brackets) for the region indicated in the left column.

TABLE 6 NS4 sequences of the different genotypes SYNTHETIC PEPTIDE NS4-1SYNTHETIC PEPTIDE NS4-5 SYNTHETIC PEPTIDE NS4-7 prototype         (NS4a)        (NS4b)         (NS4b) position-> TYPE   1690       1700        1720       1730       1730         1740          ** *  **   **              *   *  *  *   *  *  * HCV-I 1a LSG KPAIIPDREV LYREFDESQHLPYIEQ GMMLAEQFKQ K LAEQFKQ KALGLLQTAS RQA (SEQ ID NO:272) (SEQ IDNO:273) (SEQ ID NO:274) HCV-J 1b LSG RPAVIPDREV LYQEFDE ASHLPYIEQGMQLAEQFKQ K LAEQFKQ KALGLLQTAT KQA (SEQ ID NO:275) (SEQ ID NO:276) (SEQID NO:277) HC-J6 2a VNQ RAVVAPDKEV LYEAFDE ASRAALIEE GQRIAEMLKS KIAEMLKS KIQGLLQQAS KQA (SEQ ID NO:278) (SEQ ID NO:279) (SEQ ID NO:280)HC-J8 2b LND RVVVAPDKEI LYEAFDE ASKAALIEE GQRMAEMLKS KMAEMLKS KIQGLLQQAT RQA (SEQ ID NO:281) (SEQ ID NO:282) (SEQ ID NO:283)BR36 3a LGG KPAIVPDKEV LYQQYDE SQAAPYIEQ AQVIAHQFKE K IAHQFKE KVLGLLQRATQQQ (SEQ ID NO:97) (SEQ ID NO:99) (SEQ ID NO:100) PC 5  LSGKPAIIPDREA LYQQFDE AASLPYMDE TRAIAGQFKE K IAGQFKE KVLGFISTTG QKA       V(SEQ ID NO:284) (SEQ ID NO:105) (SEQ ID NO:102 and SEQ ID NO:103,respectively) *, residues conserved in every genotype. Double underlinedamino acids are type-specific, amino acids in italics are unique to type3 and 5 sequences.

TABLE 7 SEQ ID Primer NO NO (polarity) Sequence from 5′ to 3′ 63HCPr161(+) 5′-ACCGGAGGCCAGGAGAGTGATCTCCTCC-3′ 64 HCPr162(−)5′-GGGCTGCTCTATCCTCATCGACGCCATC-3′ 65 HCPr163(+)5′-GCCAGAGGCTCGGAAGGCGATCAGCGCT-3′ 66 HCPr164(−)5′-GAGCTGCTCTGTCCTCCTCGACGCCGCA-3′ 67 HCPr23(+)5′-CTCATGGGGTACATTCCGCT-3′ 68 HCPr54(−)5′-CTATTACCAGTTCATCATCATATCCCA-3′ 69 HCPr116(+)5′-ttttAAATACATCATGRCITGYATG-3′ 70 HCPr66(−)5′-ctattaTTGTATCCCRCTGATGAARTTCCACAT-3′ 71 HCPr118(−)5′actagtcgactaYTGIATICCRCTIATRWARTTCCACAT-3′ 72 HCPr117(+)5′-ttttAAATACATCGCIRCITGCATGCA-3′ 73 HcPr119(−)5′-actagtcgactaRTTIGCIATIAGCCKRTTCATCCAYTG-3′ 74 HCPr131(+)5′-ggaattctagaCCITCITGGGAYGARAYITGGAARTG-3′ 75 HCPr130(+)5′-ggaattctagACIGCITAYCARGCIACIGTITGYGC-3′ 76 HCPr134(+)5′-CATATAGATGCCCACTTCCTATC-3′ 77 HCPr3(+) 5′-GTGTGCCAGGACCATC-3′ 78HCPr4(−) 5′-GACATGCATGTCATGATGTA-3′ 79 HCPr152(+)5′-TACGCCTCTTCTATATCGGTTGGGGCCTG-3′ 80 HCPr52(+)5′-atgTTGGGTAAGGTCATCGATACCCT-3′ 81 HCPr41(+)5′-CCCGGGAGGTCTCGTAGACCGTGCA-3′ 82 HCPr40(−)5′-ctattaAAGATAGAGAAAGAGCAACCGGG-3′ 124 HCPR2065′-tggggatcccgtatgatacccgctgctttga-3′ 125 HCPR2075′-ggcggaattcctggtcatagcctccgtgaa-3′ 141 HCPR1095′-tgggatatgatgatgaactggtc-3′ 142 HCPR14 5′-ccaggtacaaccgaaccaattgcc-3′

TABLE 8 NS4 SEROTYPING Type 1 NS4 Type 2 NS4 Type 3 NS4 serum 1 5 7 1 57 1 5 7 type 1a 101 3 3 3 − 1 3 +/− +/− 3 102 1 +/− 2 − − 2 − − 1 103 13 3 − +/− 3 − +/− 3 104 3 3 3 2 2 3 3 +/− 2 105 3 3 3 − 2 2 +/− +/− 2106 3 1 1 − 1 2 +/− +/− +/− 107 3 3 3 − 2 2 2 − 1 108 3 3 3 − +/− 2 +/−1 2 109 3 3 3 +/− 2 3 1 − 3 110 3 3 3 − +/− 1 − − 3 type 1b 111 +/− +/−− − − − − − − 112 − 2 3 − − 2 − − 3 113 2 3 3 − − 1 − − 3 114 2 3 3 1 +2 + 1 3 115 3 3 3 − + 3 − − 3 116 3 3 3 − +/− 1 − − 1 117 3 − − 3 +/−+/− +/− − − 118 1 2 3 − +/− 2 − +/− 3 119 +/− 2 2 +/− +/− 2 + 1 2 120 −3 3 −     3 +/− +/− − − − 121 3 3 3 +/− 2 2 2 2 3 122 3 3 1 − 1 2 2 1 1123 3 3 2 − 1 2 − 1 1 124 3 3 3 +/− 2 − − 2 125 3 3 3 1 1 3 2 1 3 126 12 2 1 1 1 1 1 1 127 3 2 +/− − +/− 1 +/− +/− +/− 128 3 3 3 − +/− 1 2 +/−+/− 129 2 3 3 − − 3 − − 3 130 − 2 1 +/− − − − − − 131 − 1 1 − − − − −+/− 132 − − − +/− − +/− +/− − − 133 3 3 3 − 1 3 − 1 3 134 − 2 2 − − − −− − 135 3 3 3 1 + 2 2 1 3 136 − 3 3 +/− +/− +/− +/− − 3 137 +/− +/− +/−+/− +/− +/− +/− − − 138 3 3 3 +/− 2 2 1 + 3 type 2a 139 3 − − 3 3 +/− 1− − 140 +/− − − 3 3 3 3 − − 141 2 − − 2 1 +/− 2 − − 142 − − − − +/− − −− − 143 − +/− +/− 1 2 1 1 +/− +/− 144 1 1 + 1 3 2 1 1 2 145 − +/− +/− 31 2 2 +/− +/− 146 − − − +/− +/− − − − − 147 − +/− − 3 1 3 − − − 148 − −− +/− − − +/− − − type 2b 149 − +/− +/− 3 3 1 2 +/− +/− type 3 150 +/−+/− +/− +/− +/− +/− 1 3 3 151 − − − − − − 2 − 2 152 +/− − − − − − 3 − −153 − − − − − − − 1 − 154 +/− 1 3 − +/− 2 2 1 3 155 − 2 3 − 2 2 1 1 3156 − − − − − − − − − 157 − − − +/− +/− − +/− 2 2 158 2 − − − 1 2 3 2 2159 − − − − +/− +/− − 3 3 160 − − − − +/− − − 2 3 161 − − − − 1 1 +/− 32 type 4 162 1 − − − − − − − − 163 2 − − − +/− +/− +/− − −

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284 1 213 DNA hepatitis C virus 1 ctcacggaac ggctttactg cgggggccctatgttcaaca gcaagggggc ccagtgtggt 60 tatcgccgct gccgtgccag tggagttctgcctaccagct tcggcaacac aatcacttgc 120 tacatcaagg ccacagcggc tgcaagggccgcaggcctcc ggaacccgga ctttcttgtc 180 tgcggagatg atctggtcgt ggtggctgagagt 213 2 71 PRT hepatitis C virus 2 Leu Thr Glu Arg Leu Tyr Cys Gly GlyPro Met Phe Asn Ser Lys Gly 1 5 10 15 Ala Gln Cys Gly Tyr Arg Arg CysArg Ala Ser Gly Val Leu Pro Thr 20 25 30 Ser Phe Gly Asn Thr Ile Thr CysTyr Ile Lys Ala Thr Ala Ala Ala 35 40 45 Arg Ala Ala Gly Leu Arg Asn ProAsp Phe Leu Val Cys Gly Asp Asp 50 55 60 Leu Val Val Val Ala Glu Ser 6570 3 213 DNA hepatitis C virus 3 ctcacggaac ggctttactg cgggggccctatgttcaaca gcaagggggc ccagtgtggt 60 tatcgccgct gccgtgccag tggagttctgcctaccagct tcggcaacac aatcacttgc 120 tacatcaagg ccacagcggc tgcaagggccgcaggcctcc ggaacccgga ctttcttgtc 180 tgcggagatg atctggtcgt ggtggctgagagt 213 4 71 PRT hepatitis C virus 4 Leu Thr Glu Arg Leu Tyr Cys Gly GlyPro Met Phe Asn Ser Lys Gly 1 5 10 15 Ala Gln Cys Gly Tyr Arg Arg CysArg Ala Ser Gly Val Leu Pro Thr 20 25 30 Ser Phe Gly Asn Thr Ile Thr CysTyr Ile Lys Ala Thr Ala Ala Ala 35 40 45 Lys Ala Ala Gly Leu Arg Asn ProAsp Phe Leu Val Cys Gly Asp Asp 50 55 60 Leu Val Val Val Ala Glu Ser 6570 5 213 DNA hepatitis C virus 5 ctcacggagc ggctttactg cgggggccctatgtttaaca gcaagggggc ccagtgtggt 60 tatcgccgtt gccgtgccag tggagttctgcctaccagct tcggcaacac aatcacttgt 120 tacatcaaag ccacagcggc cgcaaaagccgcaggcctcc ggagcccgga ctttcttgtc 180 tgcggagatg atctggtcgt ggtggctgagagt 213 6 71 PRT hepatitis C virus 6 Leu Thr Glu Arg Leu Tyr Cys Gly GlyPro Met Phe Asn Ser Lys Gly 1 5 10 15 Ala Gln Cys Gly Tyr Arg Arg CysArg Ala Ser Gly Val Leu Pro Thr 20 25 30 Ser Phe Gly Asn Thr Ile Thr CysTyr Ile Lys Ala Thr Ala Ala Ala 35 40 45 Lys Ala Ala Gly Leu Arg Ser ProAsp Phe Leu Val Cys Gly Asp Asp 50 55 60 Leu Val Val Val Ala Glu Ser 6570 7 213 DNA hepatitis C virus 7 ctcacggagc ggctttactg cgggggccctatgtttaaca gcaaaggggc ccagtgtggt 60 tatcgccgtt gccgtgccag tggagttctgcctaccagct tcggcaacac aatcacttgt 120 tacatcaaag ccacagcggc cgcaaaagccgcaggcctcc ggagcccgga ctttcttgtc 180 tgcggagatg atctggtcgt ggtggctgagagt 213 8 71 PRT hepatitis C virus 8 Leu Thr Glu Arg Leu Tyr Cys Gly GlyPro Met Phe Asn Ser Lys Gly 1 5 10 15 Ala Gln Cys Gly Tyr Arg Arg CysArg Ala Ser Gly Val Leu Pro Thr 20 25 30 Ser Phe Gly Asn Thr Ile Thr CysTyr Ile Lys Ala Thr Ala Ala Ala 35 40 45 Lys Ala Ala Gly Leu Arg Ser ProAsp Phe Leu Val Cys Gly Asp Asp 50 55 60 Leu Val Val Val Ala Glu Ser 6570 9 213 DNA hepatitis C virus 9 ctcacggagc ggctttactg cgggggccctatgttcaaca gcaagggggc ccagtgtggt 60 tatcgccgtt gtcgtgccag tggagttctgcctaccagtt tcggcaacac aatcacttgt 120 tacatcaagg ccacagcggc tgcaaaagccgcaggcctcc ggaacccgga ctttcttgtt 180 tgcggagatg atttggtcgt ggtggctgagagt 213 10 71 PRT hepatitis C virus 10 Leu Thr Glu Arg Leu Tyr Cys GlyGly Pro Met Phe Asn Ser Lys Gly 1 5 10 15 Ala Gln Cys Gly Tyr Arg ArgCys Arg Ala Ser Gly Val Leu Pro Thr 20 25 30 Ser Phe Gly Asn Thr Ile ThrCys Tyr Ile Lys Ala Thr Ala Ala Ala 35 40 45 Lys Ala Ala Gly Leu Arg AsnPro Asp Phe Leu Val Cys Gly Asp Asp 50 55 60 Leu Val Val Val Ala Glu Ser65 70 11 213 DNA hepatitis C virus 11 ctcacggagc ggctttactg cgggggccctatgttcaaca gcaagggggc ccagtgtggt 60 tatcgccgtt gtcgtgccag tggagttctgcctaccagtt tcggcaacac aatcacttgt 120 tacatcaagg ccacagcggc tgcaaaagccgcaggcctcc ggaacccgga ctttcttgtt 180 tgcggagatg atttggtcgt ggtggctgagagt 213 12 71 PRT hepatitis C virus 12 Leu Thr Glu Arg Leu Tyr Cys GlyGly Pro Met Phe Asn Ser Lys Gly 1 5 10 15 Ala Gln Cys Gly Tyr Arg ArgCys Arg Ala Ser Gly Val Leu Pro Thr 20 25 30 Ser Phe Gly Asn Thr Ile ThrCys Tyr Ile Lys Ala Thr Ala Ala Ala 35 40 45 Lys Ala Ala Gly Leu Arg AsnPro Asp Phe Leu Val Cys Gly Asp Asp 50 55 60 Leu Val Val Val Ala Glu Ser65 70 13 541 DNA hepatitis C virus 13 cgtcggcgct cctgtaggag gcgtcgcaagagcccttgcg catggcgtga gggcccttga 60 agacgggata aatttcgcaa cagggaatttgcccggttgc tccttttcta tcttccttct 120 tgctctgttc tcttgcttaa tccatccagcagctagtcta gagtggcgga acacgtctgg 180 cctctatgtc cttaccaacg actgttccaatagcagtatt gtgtatgagg ccgatgacgt 240 tattctgcac acacccggct gtgtaccttgtgttcaggac ggtaatacat ctgcgtgctg 300 gaccccagtg acacctacag tggcagtcaggtacgtcgga gcaaccaccg cttcgatacg 360 caggcatgta gacatgttgg tgggcgcggccacgatgtgc tctgctctct acgtgggtga 420 tatgtgtggg gccgtcttcc tcgtgggacaagccttcacg ttcagacctc gtcgccatca 480 aacggtccag acctgtaact gctcactgtacccaggccat ctttcaggac accgaatggc 540 t 541 14 180 PRT hepatitis C virus14 Val Gly Ala Pro Val Gly Gly Val Ala Arg Ala Leu Ala His Gly Val 1 510 15 Arg Ala Leu Glu Asp Gly Ile Asn Phe Ala Thr Gly Asn Leu Pro Gly 2025 30 Cys Ser Phe Ser Ile Phe Leu Leu Ala Leu Phe Ser Cys Leu Ile His 3540 45 Pro Ala Ala Ser Leu Glu Trp Arg Asn Thr Ser Gly Leu Tyr Val Leu 5055 60 Thr Asn Asp Cys Ser Asn Ser Ser Ile Val Tyr Glu Ala Asp Asp Val 6570 75 80 Ile Leu His Thr Pro Gly Cys Val Pro Cys Val Gln Asp Gly Asn Thr85 90 95 Ser Ala Cys Trp Thr Pro Val Thr Pro Thr Val Ala Val Arg Tyr Val100 105 110 Gly Ala Thr Thr Ala Ser Ile Arg Arg His Val Asp Met Leu ValGly 115 120 125 Ala Ala Thr Met Cys Ser Ala Leu Tyr Val Gly Asp Met CysGly Ala 130 135 140 Val Phe Leu Val Gly Gln Ala Phe Thr Phe Arg Pro ArgArg His Gln 145 150 155 160 Thr Val Gln Thr Cys Asn Cys Ser Leu Tyr ProGly His Leu Ser Gly 165 170 175 His Arg Met Ala 180 15 541 DNA hepatitisC virus 15 cgtcggcgct cctgtaggag gcgtcgcaag agcccttgcg catggcgtgagggcccttga 60 agacgggata aatttcgcaa cagggaattt gcccggttgc tccttttctatcttccttcc 120 tgctctgttc tcttgcttaa tccatccagc agctagtcta gagtggcggaacacgtctgg 180 cctctatgtc cttaccaacg actgttccaa tagcagtatt gtgtatgaggccgatgacgt 240 tattctgcac acacccggct gtgtaccttg tgttcaggac ggtaatacatctgcgtgctg 300 gaccccagtg acacctacag tggcagtcag gtacgtcgga gcaaccaccgcttcgatacg 360 caggcatgta gacatattgg tgggcgcggc cacaatgtgc tctgctctctacgtgggtga 420 tatgtgtggg gccgtcttcc tcgtgggaca agccttcacg ttcagacctcgtcgccatca 480 aacggtccag acctgtaact gctcactgta cccaggccat ctttcaggacaccgaatggc 540 t 541 16 180 PRT hepatitis C virus 16 Val Gly Ala Pro ValGly Gly Val Ala Arg Ala Leu Ala His Gly Val 1 5 10 15 Arg Ala Leu GluAsp Gly Ile Asn Phe Ala Thr Gly Asn Leu Pro Gly 20 25 30 Cys Ser Phe SerIle Phe Leu Pro Ala Leu Phe Ser Cys Leu Ile His 35 40 45 Pro Ala Ala SerLeu Glu Trp Arg Asn Thr Ser Gly Leu Tyr Val Leu 50 55 60 Thr Asn Asp CysSer Asn Ser Ser Ile Val Tyr Glu Ala Asp Asp Val 65 70 75 80 Ile Leu HisThr Pro Gly Cys Val Pro Cys Val Gln Asp Gly Asn Thr 85 90 95 Ser Ala CysTrp Thr Pro Val Thr Pro Thr Val Ala Val Arg Tyr Val 100 105 110 Gly AlaThr Thr Ala Ser Ile Arg Arg His Val Asp Ile Leu Val Gly 115 120 125 AlaAla Thr Met Cys Ser Ala Leu Tyr Val Gly Asp Met Cys Gly Ala 130 135 140Val Phe Leu Val Gly Gln Ala Phe Thr Phe Arg Pro Arg Arg His Gln 145 150155 160 Thr Val Gln Thr Cys Asn Cys Ser Leu Tyr Pro Gly His Leu Ser Gly165 170 175 His Arg Met Ala 180 17 541 DNA hepatitis C virus 17cgtcggcgct cctgtaggag gcgtcgcaag agcccttgcg catggcgtga gggcccttga 60agacgggata aatttcgcaa cagggaattt gcccggttgc tccttttcta tcttccttct 120tgctctgttc tcttgcttaa tccatccagc agctagtcta gagtggcgga acacgtctgg 180cctctacgtc cttaccaacg actgttccaa tagcagtatt gtgtatgagg ccgatgacgt 240tattctgcac acacccggct gtgtaccttg tgttcaggac ggtaatacat ctgcgtgctg 300gaccccagtg acacctacag tggcagtcag gtacgtcgga gcaaccaccg cttcgatacg 360caggcatgta gacatattgg tgggcgcggc cacgatgtgc tctgctctct acgtgggtga 420tatgtgtggg gccgtcttcc tcgtgggaca agccttcacg ttcagacctc gtcgccatca 480aacggtccag acctgtaact gctcactgta cccaggccat ctttcaggac accgaatggc 540 t541 18 180 PRT hepatitis C virus 18 Val Gly Ala Pro Val Gly Gly Val AlaArg Ala Leu Ala His Gly Val 1 5 10 15 Arg Ala Leu Glu Asp Gly Ile AsnPhe Ala Thr Gly Asn Leu Pro Gly 20 25 30 Cys Ser Phe Ser Ile Phe Leu LeuAla Leu Phe Ser Cys Leu Ile His 35 40 45 Pro Ala Ala Ser Leu Glu Trp ArgAsn Thr Ser Gly Leu Tyr Val Leu 50 55 60 Thr Asn Asp Cys Ser Asn Ser SerIle Val Tyr Glu Ala Asp Asp Val 65 70 75 80 Ile Leu His Thr Pro Gly CysVal Pro Cys Val Gln Asp Gly Asn Thr 85 90 95 Ser Ala Cys Trp Thr Pro ValThr Pro Thr Val Ala Val Arg Tyr Val 100 105 110 Gly Ala Thr Thr Ala SerIle Arg Arg His Val Asp Ile Leu Val Gly 115 120 125 Ala Ala Thr Met CysSer Ala Leu Tyr Val Gly Asp Met Cys Gly Ala 130 135 140 Val Phe Leu ValGly Gln Ala Phe Thr Phe Arg Pro Arg Arg His Gln 145 150 155 160 Thr ValGln Thr Cys Asn Cys Ser Leu Tyr Pro Gly His Leu Ser Gly 165 170 175 HisArg Met Ala 180 19 541 DNA hepatitis C virus 19 cgtcggcgct cccgtaggaggcgtcgcaag agcccttgcg catggcgtga gggcccttga 60 agacgggata aatttcgcaacagggaattt gcccggttgc tccttttcta ttttccttct 120 tgctctgttc tcttgcttaattcatccagc agctagtcta gagtggcgga atacgtctgg 180 cctctatgtc cttaccaacgactgttccaa tagcagtatt gtgtacgagg ccgatgacgt 240 tattctgcac acacccggctgcataccttg tgtccaggac ggcaatacat ccacgtgctg 300 gaccccagtg acacctacagtggcagtcaa gtacgtcgga gcaaccaccg cttcgatacg 360 cagtcatgtg gacctattagtgggcgcggc cacgatgtgc tcagcgctct acgtgggtga 420 tatgtgtggg gccgtcttccttgtgggaca agccttcacg ttcagacctc gtcgccatca 480 aacggtccag acctgtaactgctcgctgta cccaggccat ctttcaggac atcgaatggc 540 t 541 20 180 PRThepatitis C virus 20 Val Gly Ala Pro Val Gly Gly Val Ala Arg Ala Leu AlaHis Gly Val 1 5 10 15 Arg Ala Leu Glu Asp Gly Ile Asn Phe Ala Thr GlyAsn Leu Pro Gly 20 25 30 Cys Ser Phe Ser Ile Phe Leu Leu Ala Leu Phe SerCys Leu Ile His 35 40 45 Pro Ala Ala Ser Leu Glu Trp Arg Asn Thr Ser GlyLeu Tyr Val Leu 50 55 60 Thr Asn Asp Cys Ser Asn Ser Ser Ile Val Tyr GluAla Asp Asp Val 65 70 75 80 Ile Leu His Thr Pro Gly Cys Ile Pro Cys ValGln Asp Gly Asn Thr 85 90 95 Ser Thr Cys Trp Thr Pro Val Thr Pro Thr ValAla Val Lys Tyr Val 100 105 110 Gly Ala Thr Thr Ala Ser Ile Arg Ser HisVal Asp Leu Leu Val Gly 115 120 125 Ala Ala Thr Met Cys Ser Ala Leu TyrVal Gly Asp Met Cys Gly Ala 130 135 140 Val Phe Leu Val Gly Gln Ala PheThr Phe Arg Pro Arg Arg His Gln 145 150 155 160 Thr Val Gln Thr Cys AsnCys Ser Leu Tyr Pro Gly His Leu Ser Gly 165 170 175 His Arg Met Ala 18021 541 DNA hepatitis C virus 21 cgtcggcgct cccgtaggag gcgtcgcaagagcccttgcg catggcgtga gggcccttga 60 agacgggata aatttcgcaa cagggaatttgcccggttgc tccttttcta ttttccttct 120 tgctctgttc tcttgcttaa ttcatccagcagctagtcta gagtggcgga atacgtctgg 180 cctctatgtc cttaccaacg actgttccaatagcagtatt gtgtacgagg ccgatgacgt 240 tattctgcac acacccggct gcataccttgtgtccaggac ggcaatacat ccacgtgctg 300 gaccccagtg acacctacag tggcagtcaagtacgtcgga gcaaccaccg cttcgatacg 360 cagtcatgtg gacctattag tgggcgcggccacgatgtgc tctgcgctct acgtgggtga 420 catgtgtggg gctgtcttcc tcgtgggacaagccttcacg ttcagacctc gtcgccatca 480 aacggtccag acctgtaact gctcgctgtacccaggccat ctttcaggac atcgaatggc 540 t 541 22 180 PRT hepatitis C virus22 Val Gly Ala Pro Val Gly Gly Val Ala Arg Ala Leu Ala His Gly Val 1 510 15 Arg Ala Leu Glu Asp Gly Ile Asn Phe Ala Thr Gly Asn Leu Pro Gly 2025 30 Cys Ser Phe Ser Ile Phe Leu Leu Ala Leu Phe Ser Cys Leu Ile His 3540 45 Pro Ala Ala Ser Leu Glu Trp Arg Asn Thr Ser Gly Leu Tyr Val Leu 5055 60 Thr Asn Asp Cys Ser Asn Ser Ser Ile Val Tyr Glu Ala Asp Asp Val 6570 75 80 Ile Leu His Thr Pro Gly Cys Ile Pro Cys Val Gln Asp Gly Asn Thr85 90 95 Ser Thr Cys Trp Thr Pro Val Thr Pro Thr Val Ala Val Lys Tyr Val100 105 110 Gly Ala Thr Thr Ala Ser Ile Arg Ser His Val Asp Leu Leu ValGly 115 120 125 Ala Ala Thr Met Cys Ser Ala Leu Tyr Val Gly Asp Met CysGly Ala 130 135 140 Val Phe Leu Val Gly Gln Ala Phe Thr Phe Arg Pro ArgArg His Gln 145 150 155 160 Thr Val Gln Thr Cys Asn Cys Ser Leu Tyr ProGly His Leu Ser Gly 165 170 175 His Arg Met Ala 180 23 541 DNA hepatitisC virus 23 cgtcggcgct cccgtaggag gcgtcgcaag agcccttgcg catggcgtgagggcccttga 60 ggacgggata aacttcgcaa cagggaattt gcccggttgc tccttttctatcttccttct 120 tgctctgttc tcttgcttaa tccatccagc agctggtcta gagtggcggaatacgtctgg 180 cctctatgtc cttaccaacg actgttccaa tagtagtatt gtgtatgaggccgatgacgt 240 tattctgcac gcgcccggct gtgtaccttg tgtccaggac ggcaatacgtctacatgctg 300 gaccccagta acacctacag tggcagtcag gtacgtcggg gcaaccaccgcttcgatacg 360 cagtcatgtg gacctgttag taggcgcggc cacgatgtgc tctgcgctttacgtgggtga 420 tatgtgtggg gccgtcttcc tcgtgggaca agccttcacg ttcagaccccgccgccatca 480 aacggtccag acctgtaact gctcgctgta cccaggccat ctttcaggacatcgcatggc 540 t 541 24 180 PRT hepatitis C virus 24 Val Gly Ala Pro ValGly Gly Val Ala Arg Ala Leu Ala His Gly Val 1 5 10 15 Arg Ala Leu GluAsp Gly Ile Asn Phe Ala Thr Gly Asn Leu Pro Gly 20 25 30 Cys Ser Phe SerIle Phe Leu Leu Ala Leu Phe Ser Cys Leu Ile His 35 40 45 Pro Ala Ala GlyLeu Glu Trp Arg Asn Thr Ser Gly Leu Tyr Val Leu 50 55 60 Thr Asn Asp CysSer Asn Ser Ser Ile Val Tyr Glu Ala Asp Asp Val 65 70 75 80 Ile Leu HisAla Pro Gly Cys Val Pro Cys Val Gln Asp Gly Asn Thr 85 90 95 Ser Thr CysTrp Thr Pro Val Thr Pro Thr Val Ala Val Arg Tyr Val 100 105 110 Gly AlaThr Thr Ala Ser Ile Arg Ser His Val Asp Leu Leu Val Gly 115 120 125 AlaAla Thr Met Cys Ser Ala Leu Tyr Val Gly Asp Met Cys Gly Ala 130 135 140Val Phe Leu Val Gly Gln Ala Phe Thr Phe Arg Pro Arg Arg His Gln 145 150155 160 Thr Val Gln Thr Cys Asn Cys Ser Leu Tyr Pro Gly His Leu Ser Gly165 170 175 His Arg Met Ala 180 25 541 DNA hepatitis C virus 25cgtcggcgct cccgtaggag gcgtcgcaag agcccttgcg catggcgtga gggcccttga 60ggacgggata aacttcgcaa cagggaattt gcccggttgc tctttttcta tcttccttct 120tgctctgttc tcttgcttaa tccatccagc agctggtcta gagtggcgga atacgtctgg 180cctctatgtc cttaccaacg actgttccaa tagtagtatt gtgtatgagg ccgatgacgt 240tattctgcac gcgcccggct gtgtaccttg tgtccaggac ggcaatacgt ctacatgctg 300gaccccagta acacctacag tggcagtcag gtacgtcggg gcaaccaccg cttcgatacg 360cagtcatgtg gacctgttag taggcgcggc cacgatgtgc tctgcgcttt acgtgggtga 420tatgtgtggg gccgtcttcc tcgtgggaca agccttcacg ttcagacccc gccgccatca 480aacggtccag acctgtaact gctcgctgta cccaggccat ctttcaggac atcgaatggc 540 t541 26 180 PRT hepatitis C virus 26 Val Gly Ala Pro Val Gly Gly Val AlaArg Ala Leu Ala His Gly Val 1 5 10 15 Arg Ala Leu Glu Asp Gly Ile AsnPhe Ala Thr Gly Asn Leu Pro Gly 20 25 30 Cys Ser Phe Ser Ile Phe Leu LeuAla Leu Phe Ser Cys Leu Ile His 35 40 45 Pro Ala Ala Gly Leu Glu Trp ArgAsn Thr Ser Gly Leu Tyr Val Leu 50 55 60 Thr Asn Asp Cys Ser Asn Ser SerIle Val Tyr Glu Ala Asp Asp Val 65 70 75 80 Ile Leu His Ala Pro Gly CysVal Pro Cys Val Gln Asp Gly Asn Thr 85 90 95 Ser Thr Cys Trp Thr Pro ValThr Pro Thr Val Ala Val Arg Tyr Val 100 105 110 Gly Ala Thr Thr Ala SerIle Arg Ser His Val Asp Leu Leu Val Gly 115 120 125 Ala Ala Thr Met CysSer Ala Leu Tyr Val Gly Asp Met Cys Gly Ala 130 135 140 Val Phe Leu ValGly Gln Ala Phe Thr Phe Arg Pro Arg Arg His Gln 145 150 155 160 Thr ValGln Thr Cys Asn Cys Ser Leu Tyr Pro Gly His Leu Ser Gly 165 170 175 HisArg Met Ala 180 27 541 DNA hepatitis C virus 27 cgtcggcgct cccgtaggaggcgtcgcaag agcccttgcg catggcgtga gggcccttga 60 ggacgggata aacttcgcaacagggaattt gcccggttgc tctttttcta tcttccttct 120 tgctctgttc tcttgcttaatccatccagc agctggtcta gagtggcgga atacgtctgg 180 cctctatgtc cttaccaacgactgttccaa tagtagtatt gtgtatgagg ccgatgacgt 240 tattctgcac gcgcccggctgtgtaccttg tgtccaggac ggcaatacgt ctacatgctg 300 gaccccagta acacctacagtggcagtcag gtacgtcggg gcaaccaccg cttcgatacg 360 cagtcatgtg gacctgttagtaggcgcggc cacgatgtgc tctgcgcttt acgtgggtga 420 tatgtgtggg gccgtcttcctcgtgggaca agccttcacg ttcagacccc gccgccatca 480 aacggtccag acctgtaactgctcgctgta cccaggccat ctttcaggac atcgaatggc 540 t 541 28 180 PRThepatitis C virus 28 Val Gly Ala Pro Val Gly Gly Val Ala Arg Ala Leu AlaHis Gly Val 1 5 10 15 Arg Ala Leu Glu Asp Gly Ile Asn Phe Ala Thr GlyAsn Leu Pro Gly 20 25 30 Cys Ser Phe Ser Ile Phe Leu Leu Ala Leu Phe SerCys Leu Ile His 35 40 45 Pro Ala Ala Gly Leu Glu Trp Arg Asn Thr Ser GlyLeu Tyr Val Leu 50 55 60 Thr Asn Asp Cys Ser Asn Ser Ser Ile Val Tyr GluAla Asp Asp Val 65 70 75 80 Ile Leu His Ala Pro Gly Cys Val Pro Cys ValGln Asp Gly Asn Thr 85 90 95 Ser Thr Cys Trp Thr Pro Val Thr Pro Thr ValAla Val Arg Tyr Val 100 105 110 Gly Ala Thr Thr Ala Ser Ile Arg Ser HisVal Asp Leu Leu Val Gly 115 120 125 Ala Ala Thr Met Cys Ser Ala Leu TyrVal Gly Asp Met Cys Gly Ala 130 135 140 Val Phe Leu Val Gly Gln Ala PheThr Phe Arg Pro Arg Arg His Gln 145 150 155 160 Thr Val Gln Thr Cys AsnCys Ser Leu Tyr Pro Gly His Leu Ser Gly 165 170 175 His Arg Met Ala 18029 287 DNA hepatitis C virus 29 tagacttttg ggagagcgtc ttcactggactaactcacat agatgcccac tttctgtcac 60 agactaagca gcagggactc aacttctcgttcctgactgc ctaccaagcc actgtgtgcg 120 ctcgcgcgca ggctcctccc ccaagttgggacgagatgtg gaagtgtctc gtacggctta 180 agccaacact acatggacct acgcctcttctatatcggtt ggggcctgtc caaaatgaaa 240 tctgcttgac acaccccatc acaaaatacatcatggcatg catgtca 287 30 95 PRT hepatitis C virus 30 Asp Phe Trp GluSer Val Phe Thr Gly Leu Thr His Ile Asp Ala His 1 5 10 15 Phe Leu SerGln Thr Lys Gln Gln Gly Leu Asn Phe Ser Phe Leu Thr 20 25 30 Ala Tyr GlnAla Thr Val Cys Ala Arg Ala Gln Ala Pro Pro Pro Ser 35 40 45 Trp Asp GluMet Trp Lys Cys Leu Val Arg Leu Lys Pro Thr Leu His 50 55 60 Gly Pro ThrPro Leu Leu Tyr Arg Leu Gly Pro Val Gln Asn Glu Ile 65 70 75 80 Cys LeuThr His Pro Ile Thr Lys Tyr Ile Met Ala Cys Met Ser 85 90 95 31 401 DNAhepatitis C virus 31 tccaaaatga aatctgcttg acacaccccg tcacaaaatacattatggca tgcatgtcag 60 ctgatctgga agtaaccacc agcacctggg tgttgcttggaggggtcctc gcggccctag 120 cggcctactg cttgtcagtc ggctgcgttg taatcgtgggtcatatcgag ctggggggca 180 agccggcact cgttccagac aaggaggtgt tgtatcaacagtacgatgag atggaggagt 240 gctcgcaagc cgccccatac atcgaacaag ctcaggtaatagcccaccag ttcaaggaga 300 aaatccttgg actgctgcag cgagccaccc aacaacaagctgtcattgag cccgtaatag 360 cttccaactg gcaaaagctt gaaaccttct ggcacaagca t401 32 133 PRT hepatitis C virus 32 Gln Asn Glu Ile Cys Leu Thr His ProVal Thr Lys Tyr Ile Met Ala 1 5 10 15 Cys Met Ser Ala Asp Leu Glu ValThr Thr Ser Thr Trp Val Leu Leu 20 25 30 Gly Gly Val Leu Ala Ala Leu AlaAla Tyr Cys Leu Ser Val Gly Cys 35 40 45 Val Val Ile Val Gly His Ile GluLeu Gly Gly Lys Pro Ala Leu Val 50 55 60 Pro Asp Lys Glu Val Leu Tyr GlnGln Tyr Asp Glu Met Glu Glu Cys 65 70 75 80 Ser Gln Ala Ala Pro Tyr IleGlu Gln Ala Gln Val Ile Ala His Gln 85 90 95 Phe Lys Glu Lys Ile Leu GlyLeu Leu Gln Arg Ala Thr Gln Gln Gln 100 105 110 Ala Val Ile Glu Pro ValIle Ala Ser Asn Trp Gln Lys Leu Glu Thr 115 120 125 Phe Trp His Lys His130 33 401 DNA hepatitis C virus 33 tccaaaatga aatctgcttg acacaccccgtcacaaaata cattatggca tgcatgtcag 60 ctgatctgga agtaaccacc agcacctgggtgttgcttgg aggggtcctc gcggccctag 120 cggcctactg cttgtcagtc ggctgcgttgtaatcgtggg tcatatcgag ctggggggca 180 agccggcact cgttccagac aaggaggtgttgtatcaaca gtacgatgag atggaggagt 240 gctcgcaagc cgccccatac atcgaacaagctcaggtaat agcccaccag ttcaaggaga 300 aaatccttgg actgctgcag cgagccacccaacaacaagc tgtcattgag cccgtaatag 360 cttccaactg gcaaaagctt gaaaccttctggcacaagca t 401 34 133 PRT hepatitis C virus 34 Gln Asn Glu Ile Cys LeuThr His Pro Val Thr Lys Tyr Ile Met Ala 1 5 10 15 Cys Met Ser Ala AspLeu Glu Val Thr Thr Ser Thr Trp Val Leu Leu 20 25 30 Gly Gly Val Leu AlaAla Leu Ala Ala Tyr Cys Leu Ser Val Gly Cys 35 40 45 Val Val Ile Val GlyHis Ile Glu Leu Gly Gly Lys Pro Ala Leu Val 50 55 60 Pro Asp Lys Glu ValLeu Tyr Gln Gln Tyr Asp Glu Met Glu Glu Cys 65 70 75 80 Ser Gln Ala AlaPro Tyr Ile Glu Gln Ala Gln Val Ile Ala His Gln 85 90 95 Phe Lys Glu LysIle Leu Gly Leu Leu Gln Arg Ala Thr Gln Gln Gln 100 105 110 Ala Val IleGlu Pro Val Ile Ala Ser Asn Trp Gln Lys Leu Glu Thr 115 120 125 Phe TrpHis Lys His 130 35 401 DNA hepatitis C virus 35 tccaaaatga aatctgcttgacacacccca tcacaaaata catcatggca tgcatgtcag 60 ctgatctgga agtaaccaccagcacctggg ttttgcttgg aggggtcctc gcggccctag 120 cggcctactg cttgtcagtcggttgtgttg tgattgtggg tcatatcgag ctggggggca 180 agccggcaat cgttccagacaaagaggtgt tgtatcaaca atacgatgag atggaagagt 240 gctcacaagc tgccccatatatcgaacaag ctcaggtaat agctcaccag ttcaagggaa 300 aagtccttgg attgctgcagcgagccaccc aacaacaagc tgtcattgag cccatagtaa 360 ctaccaactg gcaaaagcttgaggcctttt ggcacaagca t 401 36 133 PRT hepatitis C virus 36 Gln Asn GluIle Cys Leu Thr His Pro Ile Thr Lys Tyr Ile Met Ala 1 5 10 15 Cys MetSer Ala Asp Leu Glu Val Thr Thr Ser Thr Trp Val Leu Leu 20 25 30 Gly GlyVal Leu Ala Ala Leu Ala Ala Tyr Cys Leu Ser Val Gly Cys 35 40 45 Val ValIle Val Gly His Ile Glu Leu Gly Gly Lys Pro Ala Ile Val 50 55 60 Pro AspLys Glu Val Leu Tyr Gln Gln Tyr Asp Glu Met Glu Glu Cys 65 70 75 80 SerGln Ala Ala Pro Tyr Ile Glu Gln Ala Gln Val Ile Ala His Gln 85 90 95 PheLys Gly Lys Val Leu Gly Leu Leu Gln Arg Ala Thr Gln Gln Gln 100 105 110Ala Val Ile Glu Pro Ile Val Thr Thr Asn Trp Gln Lys Leu Glu Ala 115 120125 Phe Trp His Lys His 130 37 401 DNA hepatitis C virus 37 tccaaaatgaaatctgcttg acacacccca tcacaaaata catcatggca tgcatgtcag 60 ctgatctggaagtaaccacc agcacctggg ttttgcttgg aggggtcctc gcggccctag 120 cggcctactgcttgtcagtc ggttgtgttg tgattgtggg tcatatcgag ctggggggca 180 agccggcaatcgttccagac aaagaggtgt tgtatcaaca atacgatgag atggaagagt 240 gctcacaagctgccccatat atcgaacaag ctcaggtgat agctcaccag ttcaaggaaa 300 aagtccttggattgctgcag cgagccaccc aacaacaagc tgtcattgag cccatagtaa 360 ctaccaactggcaaaagctt gaggcctttt ggcacaagca t 401 38 133 PRT hepatitis C virus 38Gln Asn Glu Ile Cys Leu Thr His Pro Ile Thr Lys Tyr Ile Met Ala 1 5 1015 Cys Met Ser Ala Asp Leu Glu Val Thr Thr Ser Thr Trp Val Leu Leu 20 2530 Gly Gly Val Leu Ala Ala Leu Ala Ala Tyr Cys Leu Ser Val Gly Cys 35 4045 Val Val Ile Val Gly His Ile Glu Leu Gly Gly Lys Pro Ala Ile Val 50 5560 Pro Asp Lys Glu Val Leu Tyr Gln Gln Tyr Asp Glu Met Glu Glu Cys 65 7075 80 Ser Gln Ala Ala Pro Tyr Ile Glu Gln Ala Gln Val Ile Ala His Gln 8590 95 Phe Lys Glu Lys Val Leu Gly Leu Leu Gln Arg Ala Thr Gln Gln Gln100 105 110 Ala Val Ile Glu Pro Ile Val Thr Thr Asn Trp Gln Lys Leu GluAla 115 120 125 Phe Trp His Lys His 130 39 401 DNA hepatitis C virus 39tccaaaatga aatctgcttg acacacccca tcacaaaata catcatggca tgcatgtcag 60ctgatctgga agtaaccacc agcacctggg ttttgcttgg aggggtcctc gcggccctag 120cggcctactg cttgtcagtc ggttgtgttg tgattgtggg tcatatcgag ctggggggca 180agccggcaat cgttccagac aaagaggtgt tgtatcaaca atacgatgag atggaagagt 240gctcacaagc tgccccatat atcgaacaag ctcaggtaat agctcaccag ttcaaggaaa 300aagtccttgg attgctgcag cgagccaccc aacaacaagc tgtcattgag cccatagtaa 360ctaccaactg gcaaaagctt gaggcctttt ggcacaagca t 401 40 133 PRT hepatitis Cvirus 40 Gln Asn Glu Ile Cys Leu Thr His Pro Ile Thr Lys Tyr Ile Met Ala1 5 10 15 Cys Met Ser Ala Asp Leu Glu Val Thr Thr Ser Thr Trp Val LeuLeu 20 25 30 Gly Gly Val Leu Ala Ala Leu Ala Ala Tyr Cys Leu Ser Val GlyCys 35 40 45 Val Val Ile Val Gly His Ile Glu Leu Gly Gly Lys Pro Ala IleVal 50 55 60 Pro Asp Lys Glu Val Leu Tyr Gln Gln Tyr Asp Glu Met Glu GluCys 65 70 75 80 Ser Gln Ala Ala Pro Tyr Ile Glu Gln Ala Gln Val Ile AlaHis Gln 85 90 95 Phe Lys Glu Lys Val Leu Gly Leu Leu Gln Arg Ala Thr GlnGln Gln 100 105 110 Ala Val Ile Glu Pro Ile Val Thr Thr Asn Trp Gln LysLeu Glu Ala 115 120 125 Phe Trp His Lys His 130 41 509 DNA hepatitis Cvirus 41 ccatgagcac gaatcctaaa cctcaaagaa aaaccaaaag aaacaccaaccgtcgcccac 60 aggacgtcaa gttcccgggc ggtggtcaga tcgttggcgg agtttacttgttgccgcgca 120 ggggccctag gatgggtgtg cgcgcgactc ggaagacttc ggaacggtcgcaaccccgtg 180 gacggcgtca gcctattccc aaggcgcgcc agcccacggg ccggtcctggggtcaacccg 240 ggtacccttg gcccctttac gccaatgagg gcctcgggtg ggcagggtggctgctctccc 300 ctcgaggctc tcggcctaat tggggcccca atgacccccg gcgaaaatcgcgtaatttgg 360 gtaaggtcat cgatacccta acgtgcggat tcgccgatct catggggtatatcccgctcg 420 taggcggccc cattgggggc gtcgcaaggg ctctcgcaca cggtgtgagggtccttgagg 480 acggggtaaa ctatgcaaca gggaattta 509 42 169 PRT hepatitisC virus 42 Met Ser Thr Asn Pro Lys Pro Gln Arg Lys Thr Lys Arg Asn ThrAsn 1 5 10 15 Arg Arg Pro Gln Asp Val Lys Phe Pro Gly Gly Gly Gln IleVal Gly 20 25 30 Gly Val Tyr Leu Leu Pro Arg Arg Gly Pro Arg Met Gly ValArg Ala 35 40 45 Thr Arg Lys Thr Ser Glu Arg Ser Gln Pro Arg Gly Arg ArgGln Pro 50 55 60 Ile Pro Lys Ala Arg Gln Pro Thr Gly Arg Ser Trp Gly GlnPro Gly 65 70 75 80 Tyr Pro Trp Pro Leu Tyr Ala Asn Glu Gly Leu Gly TrpAla Gly Trp 85 90 95 Leu Leu Ser Pro Arg Gly Ser Arg Pro Asn Trp Gly ProAsn Asp Pro 100 105 110 Arg Arg Lys Ser Arg Asn Leu Gly Lys Val Ile AspThr Leu Thr Cys 115 120 125 Gly Phe Ala Asp Leu Met Gly Tyr Ile Pro LeuVal Gly Gly Pro Ile 130 135 140 Gly Gly Val Ala Arg Ala Leu Ala His GlyVal Arg Val Leu Glu Asp 145 150 155 160 Gly Val Asn Tyr Ala Thr Gly AsnLeu 165 43 509 DNA hepatitis C virus 43 ccatgagcac gaatcctaaa cctcaaagaaaaaccaaaag aaacaccaac cgtcgcccac 60 aggacgtcaa gttcccgggc ggtggtcagatcgttggcgg agtttacttg ttgccgcgca 120 ggggccctag gatgggtgtg cgcgcgactcggaagacttc ggaacggtcg caaccccgtg 180 gacggcgtca gcctattccc aaggcgcgccagcccacggg ccggtcctgg ggtcaacccg 240 ggtacccttg gcccctttac gccaatgagggcctcgggtg ggcagggtgg ctgctctccc 300 ctcgaggctc tcggcctaat tggggccccaatgacccccg gcgaaaatcg cgtaatttgg 360 gtaaggtcat cgatacccta acgtgcggattcgccgatct catggggtat atcccgctcg 420 taggcggccc cattgggggc gtcgcaagggctctcgcaca cggtgtgagg gtccttgagg 480 acggggtaaa ctatgcaaca gggaattta 50944 169 PRT hepatitis C virus 44 Met Ser Thr Asn Pro Lys Pro Gln Arg LysThr Lys Arg Asn Thr Asn 1 5 10 15 Arg Arg Pro Gln Asp Val Lys Phe ProGly Gly Gly Gln Ile Val Gly 20 25 30 Gly Val Tyr Leu Leu Pro Arg Arg GlyPro Arg Met Gly Val Arg Ala 35 40 45 Thr Arg Lys Thr Ser Glu Arg Ser GlnPro Arg Gly Arg Arg Gln Pro 50 55 60 Ile Pro Lys Ala Arg Gln Pro Thr GlyArg Ser Trp Gly Gln Pro Gly 65 70 75 80 Tyr Pro Trp Pro Leu Tyr Ala AsnGlu Gly Leu Gly Trp Ala Gly Trp 85 90 95 Leu Leu Ser Pro Arg Gly Ser ArgPro Asn Trp Gly Pro Asn Asp Pro 100 105 110 Arg Arg Lys Ser Arg Asn LeuGly Lys Val Ile Asp Thr Leu Thr Cys 115 120 125 Gly Phe Ala Asp Leu MetGly Tyr Ile Pro Leu Val Gly Gly Pro Ile 130 135 140 Gly Gly Val Ala ArgAla Leu Ala His Gly Val Arg Val Leu Glu Asp 145 150 155 160 Gly Val AsnTyr Ala Thr Gly Asn Leu 165 45 580 DNA hepatitis C virus 45 aacgtgcggattcgccgatc tcatggggta tatcccgctc gtaggcggcc ccattggggg 60 cgtcgcaagggctctcgcac acggtgtgag ggtccttgag gacggggtaa actatgcaac 120 agggaatttacccggttgct ctttctctat ctttattctt gctcttctct cgtgtctgac 180 cgttccggcctctgcagttc cctaccgaaa tgcctctggg atttatcatg ttaccaatga 240 ttgcccaaactcttccatag tctatgaggc agataacctg atcctacacg cacctggttg 300 cgtgccttgtgtcatgacag gtaatgtgag tagatgctgg gtccaaatta cccctacact 360 gtcagccccgagcctcggag cagtcacggc tcctcttcgg agagccgttg actacctagc 420 gggaggggctgccctctgct ccgcgttata cgtaggagac gcgtgtgggg cactattctt 480 ggtaggccaaatgttcacct ataggcctcg ccagcacgct acggtgcaga actgcaactg 540 ttccatttacagtggccatg ttaccggcca ccggatggca 580 46 193 PRT hepatitis C virus 46 ThrCys Gly Phe Ala Asp Leu Met Gly Tyr Ile Pro Leu Val Gly Gly 1 5 10 15Pro Ile Gly Gly Val Ala Arg Ala Leu Ala His Gly Val Arg Val Leu 20 25 30Glu Asp Gly Val Asn Tyr Ala Thr Gly Asn Leu Pro Gly Cys Ser Phe 35 40 45Ser Ile Phe Ile Leu Ala Leu Leu Ser Cys Leu Thr Val Pro Ala Ser 50 55 60Ala Val Pro Tyr Arg Asn Ala Ser Gly Ile Tyr His Val Thr Asn Asp 65 70 7580 Cys Pro Asn Ser Ser Ile Val Tyr Glu Ala Asp Asn Leu Ile Leu His 85 9095 Ala Pro Gly Cys Val Pro Cys Val Met Thr Gly Asn Val Ser Arg Cys 100105 110 Trp Val Gln Ile Thr Pro Thr Leu Ser Ala Pro Ser Leu Gly Ala Val115 120 125 Thr Ala Pro Leu Arg Arg Ala Val Asp Tyr Leu Ala Gly Gly AlaAla 130 135 140 Leu Cys Ser Ala Leu Tyr Val Gly Asp Ala Cys Gly Ala LeuPhe Leu 145 150 155 160 Val Gly Gln Met Phe Thr Tyr Arg Pro Arg Gln HisAla Thr Val Gln 165 170 175 Asn Cys Asn Cys Ser Ile Tyr Ser Gly His ValThr Gly His Arg Met 180 185 190 Ala 47 580 DNA hepatitis C virus 47aacgtgcgga ttcgccgatc tcatggggta tatcccgctc gtaggcggcc ccattggggg 60cgtcgcaagg gctctcgcac acggtgtgag ggtccttgag gacggggtaa actatgcaac 120agggaattta cccggttgct ctttctctat ctttattctt gctcttctct cgtgtctgac 180cgttccggcc tctgcagttc cctaccgaaa tgcctctggg atttatcatg ttaccaatga 240ttgcccaaac tcttccatag tctatgaggc agataacctg atcctacacg cacctggttg 300cgtgccttgt gtcatgacag gtaatgtgag tagatgctgg gtccaaatta cccctacact 360gtcagccccg agcctcggag cagtcacggc tcctcttcgg agagccgttg actacctagc 420gggaggggct gccctctgct ccgcgttata cgtaggagac gcgtgtgggg cactattctt 480ggtaggccaa atgttcacct ataggcctcg ccagcacgct acggtgcaga actgcaactg 540ttccatttac agtggccatg ttaccggcca ccggatggca 580 48 193 PRT hepatitis Cvirus 48 Thr Cys Gly Phe Ala Asp Leu Met Gly Tyr Ile Pro Leu Val Gly Gly1 5 10 15 Pro Ile Gly Gly Val Ala Arg Ala Leu Ala His Gly Val Arg ValLeu 20 25 30 Glu Asp Gly Val Asn Tyr Ala Thr Gly Asn Leu Pro Gly Cys SerPhe 35 40 45 Ser Ile Phe Ile Leu Ala Leu Leu Ser Cys Leu Thr Val Pro AlaSer 50 55 60 Ala Val Pro Tyr Arg Asn Ala Ser Gly Ile Tyr His Val Thr AsnAsp 65 70 75 80 Cys Pro Asn Ser Ser Ile Val Tyr Glu Ala Asp Asn Leu IleLeu His 85 90 95 Ala Pro Gly Cys Val Pro Cys Val Met Thr Gly Asn Val SerArg Cys 100 105 110 Trp Val Gln Ile Thr Pro Thr Leu Ser Ala Pro Ser LeuGly Ala Val 115 120 125 Thr Ala Pro Leu Arg Arg Ala Val Asp Tyr Leu AlaGly Gly Ala Ala 130 135 140 Leu Cys Ser Ala Leu Tyr Val Gly Asp Ala CysGly Ala Leu Phe Leu 145 150 155 160 Val Gly Gln Met Phe Thr Tyr Arg ProArg Gln His Ala Thr Val Gln 165 170 175 Asn Cys Asn Cys Ser Ile Tyr SerGly His Val Thr Gly His Arg Met 180 185 190 Ala 49 959 DNA hepatitis Cvirus 49 ccatgagcac gaatcctaaa cctcaaagaa aaaccaaaag aaacaccaaccgtcgcccac 60 aggacgtcaa gttcccgggc ggtggtcaga tcgttggcgg agtttacttgttgccgcgca 120 ggggccctag gatgggtgtg cgcgcgactc ggaagacttc ggaacggtcgcaaccccgtg 180 gacggcgtca gcctattccc aaggcgcgcc agcccacggg ccggtcctggggtcaacccg 240 ggtacccttg gcccctttac gccaatgagg gcctcgggtg ggcagggtggctgctctccc 300 ctcgaggctc tcggcctaat tggggcccca atgacccccg gcgaaaatcgcgtaatttgg 360 gtaaggtcat cgatacccta acgtgcggat tcgccgatct catggggtatatcccgctcg 420 taggcggccc cattgggggc gtcgcaaggg ctctcgcaca cggtgtgagggtccttgagg 480 acggggtaaa ctatgcaaca gggaatttac ccggttgctc tttctctatctttattcttg 540 ctcttctctc gtgtctgacc gttccggcct ctgcagttcc ctaccgaaatgcctctggga 600 tttatcatgt taccaatgat tgcccaaact cttccatagt ctatgaggcagataacctga 660 tcctacacgc acctggttgc gtgccttgtg tcatgacagg taatgtgagtagatgctggg 720 tccaaattac ccctacactg tcagccccga gcctcggagc agtcacggctcctcttcgga 780 gagccgttga ctacctagcg ggaggggctg ccctctgctc cgcgttatacgtaggagacg 840 cgtgtggggc actattcttg gtaggccaaa tgttcaccta taggcctcgccagcacgcta 900 cggtgcagaa ctgcaactgt tccatttaca gtggccatgt taccggccaccggatggca 959 50 319 PRT hepatitis C virus 50 Met Ser Thr Asn Pro LysPro Gln Arg Lys Thr Lys Arg Asn Thr Asn 1 5 10 15 Arg Arg Pro Gln AspVal Lys Phe Pro Gly Gly Gly Gln Ile Val Gly 20 25 30 Gly Val Tyr Leu LeuPro Arg Arg Gly Pro Arg Met Gly Val Arg Ala 35 40 45 Thr Arg Lys Thr SerGlu Arg Ser Gln Pro Arg Gly Arg Arg Gln Pro 50 55 60 Ile Pro Lys Ala ArgGln Pro Thr Gly Arg Ser Trp Gly Gln Pro Gly 65 70 75 80 Tyr Pro Trp ProLeu Tyr Ala Asn Glu Gly Leu Gly Trp Ala Gly Trp 85 90 95 Leu Leu Ser ProArg Gly Ser Arg Pro Asn Trp Gly Pro Asn Asp Pro 100 105 110 Arg Arg LysSer Arg Asn Leu Gly Lys Val Ile Asp Thr Leu Thr Cys 115 120 125 Gly PheAla Asp Leu Met Gly Tyr Ile Pro Leu Val Gly Gly Pro Val 130 135 140 GlyGly Val Ala Arg Ala Leu Ala His Gly Val Arg Val Leu Glu Asp 145 150 155160 Gly Val Asn Tyr Pro Thr Gly Asn Leu Pro Gly Cys Ser Phe Ser Ile 165170 175 Phe Ile Leu Ala Leu Leu Ser Cys Leu Thr Val Pro Ala Ser Ala Val180 185 190 Pro Tyr Arg Asn Ala Ser Gly Ile Tyr His Val Thr Asn Asp CysPro 195 200 205 Asn Ser Ser Ile Val Tyr Glu Ala Asp Asn Leu Ile Leu HisAla Pro 210 215 220 Gly Cys Val Pro Cys Val Met Thr Gly Asn Val Ser ArgCys Trp Val 225 230 235 240 Gln Ile Thr Pro Thr Leu Ser Ala Pro Ser LeuGly Ala Val Thr Ala 245 250 255 Pro Leu Arg Arg Ala Val Asp Tyr Leu AlaGly Gly Ala Ala Leu Cys 260 265 270 Ser Ala Leu Tyr Val Gly Asp Ala CysGly Ala Leu Phe Leu Val Gly 275 280 285 Gln Met Phe Thr Tyr Arg Pro ArgGln His Ala Thr Val Gln Asn Cys 290 295 300 Asn Cys Ser Ile Tyr Ser GlyHis Val Thr Gly His Arg Met Ala 305 310 315 51 959 DNA hepatitis C virus51 ccatgagcac gaatcctaaa cctcaaagaa aaaccaaaag aaacaccaac cgtcgcccac 60aggacgtcaa gttcccgggc ggtggtcaga tcgttggcgg agtttacttg ttgccgcgca 120ggggccctag gatgggtgtg cgcgcgactc ggaagacttc ggaacggtcg caaccccgtg 180gacggcgtca gcctattccc aaggcgcgcc agcccacggg ccggtcctgg ggtcaacccg 240ggtacccttg gcccctttac gccaatgagg gcctcgggtg ggcagggtgg ctgctctccc 300ctcgaggctc tcggcctaat tggggcccca atgacccccg gcgaaaatcg cgtaatttgg 360gtaaggtcat cgatacccta acgtgcggat tcgccgatct catggggtac atcccgctcg 420taggcggccc cgttgggggc gtcgcaaggg ctctcgcaca cggtgtgagg gtccttgagg 480acggggtaaa ctatccaaca gggaatttac ccggttgctc tttctctatc tttattcttg 540ctcttctctc gtgtctgacc gttccggcct ctgcagttcc ctaccgaaat gcctctggga 600tttatcatgt taccaatgat tgcccaaact cttccatagt ctatgaggca gataacctga 660tcctacacgc acctggttgc gtgccttgtg tcatgacagg taatgtgagt agatgctggg 720tccaaattac ccctacactg tcagccccga gcctcggagc agtcacggct cctcttcgga 780gagccgttga ctacctagcg ggaggggctg ccctctgctc cgcgttatac gtaggagacg 840cgtgtggggc actattcttg gtaggccaaa tgttcaccta taggcctcgc cagcacgcta 900cggtgcagaa ctgcaactgt tccatttaca gtggccatgt taccggccac cggatggca 959 52319 PRT hepatitis C virus 52 Met Ser Thr Asn Pro Lys Pro Gln Arg Lys ThrLys Arg Asn Thr Asn 1 5 10 15 Arg Arg Pro Gln Asp Val Lys Phe Pro GlyGly Gly Gln Ile Val Gly 20 25 30 Gly Val Tyr Leu Leu Pro Arg Arg Gly ProArg Met Gly Val Arg Ala 35 40 45 Thr Arg Lys Thr Ser Glu Arg Ser Gln ProArg Gly Arg Arg Gln Pro 50 55 60 Ile Pro Lys Ala Arg Gln Pro Thr Gly ArgSer Trp Gly Gln Pro Gly 65 70 75 80 Tyr Pro Trp Pro Leu Tyr Ala Asn GluGly Leu Gly Trp Ala Gly Trp 85 90 95 Leu Leu Ser Pro Arg Gly Ser Arg ProAsn Trp Gly Pro Asn Asp Pro 100 105 110 Arg Arg Lys Ser Arg Asn Leu GlyLys Val Ile Asp Thr Leu Thr Cys 115 120 125 Gly Phe Ala Asp Leu Met GlyTyr Ile Pro Leu Val Gly Gly Pro Val 130 135 140 Gly Gly Val Ala Arg AlaLeu Ala His Gly Val Arg Val Leu Glu Asp 145 150 155 160 Gly Val Asn TyrPro Thr Gly Asn Leu Pro Gly Cys Ser Phe Ser Ile 165 170 175 Phe Ile LeuAla Leu Leu Ser Cys Leu Thr Val Pro Ala Ser Ala Val 180 185 190 Pro TyrArg Asn Ala Ser Gly Ile Tyr His Val Thr Asn Asp Cys Pro 195 200 205 AsnSer Ser Ile Val Tyr Glu Ala Asp Asn Leu Ile Leu His Ala Pro 210 215 220Gly Cys Val Pro Cys Val Met Thr Gly Asn Val Ser Arg Cys Trp Val 225 230235 240 Gln Ile Thr Pro Thr Leu Ser Ala Pro Ser Leu Gly Ala Val Thr Ala245 250 255 Pro Leu Arg Arg Ala Val Asp Tyr Leu Ala Gly Gly Ala Ala LeuCys 260 265 270 Ser Ala Leu Tyr Val Gly Asp Ala Cys Gly Ala Leu Phe LeuVal Gly 275 280 285 Gln Met Phe Thr Tyr Arg Pro Arg Gln His Ala Thr ValGln Asn Cys 290 295 300 Asn Cys Ser Ile Tyr Ser Gly His Val Thr Gly HisArg Met Ala 305 310 315 53 959 DNA hepatitis C virus 53 ccatgagcacgaatcctaaa cctcaaagaa aaaccaaaag aaacaccaac cgtcgcccac 60 aggacgtcaagttcccgggc ggtggtcaga tcgttggcgg agtttacttg ttgccgcgca 120 ggggccctaggatgggtgtg cgcgcgactc ggaagacttc ggaacggtcg caaccccgtg 180 gacggcgtcagcctattccc aaggcgcgcc agcccacggg ccggtcctgg ggtcaacccg 240 ggtacccttggcccctttac gccaatgagg gcctcgggtg ggcagggtgg ctgctctccc 300 ctcgaggctctcggcctaat tggggcccca atgacccccg gcgaaaatcg cgtaatttgg 360 gtaaggtcatcgatacccta acgtgcggat tcgccgatct catggggtay atcccgctcg 420 taggcggccccrttgggggc gtcgcaaggg ctctcgcaca cggtgtgagg gtccttgagg 480 acggggtaaactatscaaca gggaatttac ccggttgctc tttctctatc tttattcttg 540 ctcttctctcgtgtctgacc gttccggcct ctgcagttcc ctaccgaaat gcctctggga 600 tttatcatgttaccaatgat tgcccaaact cttccatagt ctatgaggca gataacctga 660 tcctacacgcacctggttgc gtgccttgtg tcatgacagg taatgtgagt agatgctggg 720 tccaaattacccctacactg tcagccccga gcctcggagc agtcacggct cctcttcgga 780 gagccgttgactacctagcg ggaggggctg ccctctgctc cgcgttatac gtaggagacg 840 cgtgtggggcactattcttg gtaggccaaa tgttcaccta taggcctcgc cagcacgcta 900 cggtgcagaactgcaactgt tccatttaca gtggccatgt taccggccac cggatggca 959 54 319 PRThepatitis C virus 54 Met Ser Thr Asn Pro Lys Pro Gln Arg Lys Thr Lys ArgAsn Thr Asn 1 5 10 15 Arg Arg Pro Gln Asp Val Lys Phe Pro Gly Gly GlyGln Ile Val Gly 20 25 30 Gly Val Tyr Leu Leu Pro Arg Arg Gly Pro Arg MetGly Val Arg Ala 35 40 45 Thr Arg Lys Thr Ser Glu Arg Ser Gln Pro Arg GlyArg Arg Gln Pro 50 55 60 Ile Pro Lys Ala Arg Gln Pro Thr Gly Arg Ser TrpGly Gln Pro Gly 65 70 75 80 Tyr Pro Trp Pro Leu Tyr Ala Asn Glu Gly LeuGly Trp Ala Gly Trp 85 90 95 Leu Leu Ser Pro Arg Gly Ser Arg Pro Asn TrpGly Pro Asn Asp Pro 100 105 110 Arg Arg Lys Ser Arg Asn Leu Gly Lys ValIle Asp Thr Leu Thr Cys 115 120 125 Gly Phe Ala Asp Leu Met Gly Tyr IlePro Leu Val Gly Gly Pro Val 130 135 140 Gly Gly Val Ala Arg Ala Leu AlaHis Gly Val Arg Val Leu Glu Asp 145 150 155 160 Gly Val Asn Tyr Pro ThrGly Asn Leu Pro Gly Cys Ser Phe Ser Ile 165 170 175 Phe Ile Leu Ala LeuLeu Ser Cys Leu Thr Val Pro Ala Ser Ala Val 180 185 190 Pro Tyr Arg AsnAla Ser Gly Ile Tyr His Val Thr Asn Asp Cys Pro 195 200 205 Asn Ser SerIle Val Tyr Glu Ala Asp Asn Leu Ile Leu His Ala Pro 210 215 220 Gly CysVal Pro Cys Val Met Thr Gly Asn Val Ser Arg Cys Trp Val 225 230 235 240Gln Ile Thr Pro Thr Leu Ser Ala Pro Ser Leu Gly Ala Val Thr Ala 245 250255 Pro Leu Arg Arg Ala Val Asp Tyr Leu Ala Gly Gly Ala Ala Leu Cys 260265 270 Ser Ala Leu Tyr Val Gly Asp Ala Cys Gly Ala Leu Phe Leu Val Gly275 280 285 Gln Met Phe Thr Tyr Arg Pro Arg Gln His Ala Thr Val Gln AsnCys 290 295 300 Asn Cys Ser Ile Tyr Ser Gly His Val Thr Gly His Arg MetAla 305 310 315 55 354 DNA hepatitis C virus misc_feature (191)..(191)“n” is any nucleotide 55 accaccggag cttctatcac atactccact tacggcaagttccttgctga tggagggtgt 60 tcaggcggcg cgcatgacgt gatcatatgc gacgagtgccattcccagga cgccaccacc 120 attcttggga taggcactgt ccttgaccag gcagagacggctggagctag gctcgtcgtc 180 ttggccacgg ncacccctcc cggcagtgtg acaacgccccaccccaacat cgaggaagtg 240 gccctgcctc aggaggggga ggttcccttc tacggcagagccattcccct tgcttttata 300 aagggtggta ggcatctcat cttctgccat tccaagaaaaattgtgatga actc 354 56 118 PRT hepatitis C virus MISC_FEATURE (64)..(64)“Xaa” is any amino acid 56 Thr Thr Gly Ala Ser Ile Thr Tyr Ser Thr TyrGly Lys Phe Leu Ala 1 5 10 15 Asp Gly Gly Cys Ser Gly Gly Ala His AspVal Ile Ile Cys Asp Glu 20 25 30 Cys His Ser Gln Asp Ala Thr Thr Ile LeuGly Ile Gly Thr Val Leu 35 40 45 Asp Gln Ala Glu Thr Ala Gly Ala Arg LeuVal Val Leu Ala Thr Xaa 50 55 60 Thr Pro Pro Gly Ser Val Thr Thr Pro HisPro Asn Ile Glu Glu Val 65 70 75 80 Ala Leu Pro Gln Glu Gly Glu Val ProPhe Tyr Gly Arg Ala Ile Pro 85 90 95 Leu Ala Phe Ile Lys Gly Gly Arg HisLeu Ile Phe Cys His Ser Lys 100 105 110 Lys Asn Cys Asp Glu Leu 115 57354 DNA hepatitis C virus misc_feature (185)..(185) “n” is anynucleotide 57 accaccggag cttctatcac atactccact tacggcaagt tccttgctgatggagggtgt 60 tcaggcggcg cgtatgacgt gatcatatgc gacgagtgcc attcccaggacgccaccacc 120 attcttggga taggcactgt ccttgaccag gcagagacgg ctggagctaggctcgtcgtc 180 ttggncacgg ncacccctcc cggcagtgtg acaacgcccc accccaacatcgaggaagtg 240 gccctgcctc aggaggggga ggttcccttc tacggnagag ccattccccttgcttttata 300 aagggtggta ggcatctcat cttctgccat tccaagaaaa aatgtgatgaactt 354 58 133 PRT hepatitis C virus MISC_FEATURE (62)..(62) “Xaa” isany amino acid 58 Thr Thr Gly Ala Ser Ile Thr Tyr Ser Thr Tyr Gly LysPhe Leu Ala 1 5 10 15 Asp Gly Gly Cys Ser Gly Gly Ala Tyr Asp Val IleIle Cys Asp Glu 20 25 30 Cys His Ser Gln Asp Ala Thr Thr Ile Leu Gly IleGly Thr Val Leu 35 40 45 Asp Gln Ala Glu Thr Ala Gly Ala Arg Leu Val ValLeu Xaa Thr Xaa 50 55 60 Thr Pro Pro Gly Ser Val Thr Thr Pro His Pro AsnIle Glu Glu Val 65 70 75 80 Ala Leu Pro Gln Glu Gly Glu Val Pro Phe TyrXaa Arg Ala Ile Pro 85 90 95 Leu Ala Phe Ile Lys Gly Gly Arg His Leu IlePhe Cys His Ser Lys 100 105 110 Lys Lys Cys Asp Glu Leu Arg Gln Ala ThrAsp Gln Pro Gly Arg Glu 115 120 125 Arg Pro Trp Glu Tyr 130 59 357 DNAhepatitis C virus misc_feature (38)..(38) “n” is any nucleotide 59atggctttca tgtctccgga cttggaggtc attaccanca cttgggttct ggtggggggc 60gttgtggcga ccctgncgnc ctactgcttg acggtgggtt cggtagccat agtcggtagg 120atcatcctct ctgggaaacc tgccatcatt nccgataggg aggtattata ccagcaattt 180gatgagatgg aggagtgctc ggcctcgttg ccctatatgg acgaaacacg tnccattgcc 240ggacaattca aagagaaagt gctcggcttc atcagcacga ccggccagaa ggctgaaact 300ctgaagccgg cagccacgtc tgtgtggaac aaggctgatc agttctggnc cacatac 357 60128 PRT hepatitis C virus MISC_FEATURE (13)..(13) “Xaa” is any aminoacid 60 Met Ala Phe Met Ser Pro Asp Leu Glu Val Ile Thr Xaa Thr Trp Val1 5 10 15 Leu Val Gly Gly Val Val Ala Thr Leu Xaa Xaa Tyr Cys Leu ThrVal 20 25 30 Gly Ser Val Ala Ile Val Gly Arg Ile Ile Leu Ser Gly Lys ProAla 35 40 45 Ile Ile Xaa Asp Arg Glu Val Leu Tyr Gln Gln Phe Asp Glu MetGlu 50 55 60 Glu Cys Ser Ala Ser Leu Pro Tyr Met Asp Glu Thr Arg Xaa IleAla 65 70 75 80 Gly Gln Phe Lys Glu Lys Val Leu Gly Phe Ile Ser Thr ThrGly Gln 85 90 95 Lys Ala Glu Thr Leu Lys Pro Ala Ala Thr Ser Val Trp AsnLys Ala 100 105 110 Asp Gln Phe Trp Xaa Thr Tyr Met Trp Asn Phe Ile SerGly Ile Gln 115 120 125 61 357 DNA hepatitis C virus misc_feature(38)..(38) “n” is any nucleotide 61 atggcttgca tgtctgcgga cctggaggtcattaccanca cttgggttct ggtggggggc 60 gttgtggcgn ccctggcggc ctactgcttgacggtgggtt cggtagccat agtcggtagg 120 atcatcctct ctgggaaacc tgccatcattcccgataggg aggcattata ccancaattt 180 gatgagatgg aggagtgctc ggcctcgttgccctatatgg acgagacacg tgccattgcc 240 ggacaattca aagagaaagt gctcggcttcatcagcacga ccggccagaa ggctgaaact 300 ctgaagccgg cagccacgtc tgtgtggaacaaggctganc agttctgggc cacatac 357 62 128 PRT hepatitis C virusMISC_FEATURE (13)..(13) “Xaa” is any amino acid 62 Met Ala Cys Met SerAla Asp Leu Glu Val Ile Thr Xaa Thr Trp Val 1 5 10 15 Leu Val Gly GlyVal Val Ala Xaa Leu Ala Ala Tyr Cys Leu Thr Val 20 25 30 Gly Ser Val AlaIle Val Gly Arg Ile Ile Leu Ser Gly Lys Pro Ala 35 40 45 Ile Ile Pro AspArg Glu Ala Leu Tyr Xaa Gln Phe Asp Glu Met Glu 50 55 60 Glu Cys Ser AlaSer Leu Pro Tyr Met Asp Glu Thr Arg Ala Ile Ala 65 70 75 80 Gly Gln PheLys Glu Lys Val Leu Gly Phe Ile Ser Thr Thr Gly Gln 85 90 95 Lys Ala GluThr Leu Lys Pro Ala Ala Thr Ser Val Trp Asn Lys Ala 100 105 110 Xaa GlnPhe Trp Ala Thr Tyr Met Trp Asn Phe Ile Ser Gly Ile Gln 115 120 125 6328 DNA artificial misc_feature HCPr161 63 accggaggcc aggagagtga tctcctcc28 64 28 DNA artificial misc_feature HCPr162 64 gggctgctct atcctcatcgacgccatc 28 65 28 DNA artificial misc_feature HCPr163 65 gccagaggctcggaaggcga tcagcgct 28 66 28 DNA artificial misc_feature HCPr164 66gagctgctct gtcctcctcg acgccgca 28 67 20 DNA artificial misc_featureHCPr23 67 ctcatggggt acattccgct 20 68 27 DNA artificial misc_featureHCPr54 68 ctattaccag ttcatcatca tatccca 27 69 24 DNA artificialmisc_feature HCPr116 69 ttttaaatac atcatgrctg yatg 24 70 33 DNAartificial misc_feature HCPr66 70 ctattattgt atcccrctga tgaarttcca cat33 71 36 DNA artificial misc_feature HCPr118 71 actagtcgac taytgatccrctatrwartt ccacat 36 72 25 DNA artificial misc_feature HCPr117 72ttttaaatac atcgcrctgc atgca 25 73 36 DNA artificial misc_feature HCPr11973 actagtcgac tarttgcata gcckrttcat ccaytg 36 74 34 DNA artificialmisc_feature HCPr131 74 ggaattctag acctctggga ygaraytgga artg 34 75 31DNA artificial misc_feature HCPr130 75 ggaattctag acgctaycar gcacgttgygc 31 76 23 DNA artificial misc_feature HCPr134 76 catatagatg cccacttcctatc 23 77 16 DNA artificial misc_feature HCPr3 77 gtgtgccagg accatc 1678 20 DNA artificial misc_feature HCPr4 78 gacatgcatg tcatgatgta 20 7929 DNA artificial misc_feature HCPr152 79 tacgcctctt ctatatcggttggggcctg 29 80 26 DNA artificial misc_feature HCPr52 80 atgttgggtaaggtcatcga taccct 26 81 25 DNA artificial misc_feature HCPr41 81cccgggaggt ctcgtagacc gtgca 25 82 29 DNA artificial misc_feature HCPr4082 ctattaaaga tagagaaaga gcaaccggg 29 83 12 PRT hepatitis C virus 83 LeuGlu Trp Arg Asn Thr Ser Gly Leu Tyr Val Leu 1 5 10 84 12 PRT hepatitis Cvirus 84 Val Pro Tyr Arg Asn Ala Ser Gly Ile Tyr His Val 1 5 10 85 11PRT hepatitis C virus 85 Val Tyr Glu Ala Asp Asp Val Ile Leu His Thr 1 510 86 11 PRT hepatitis C virus 86 Val Tyr Glu Ala Asp Asn Leu Ile LeuHis Ala 1 5 10 87 13 PRT hepatitis C virus 87 Val Gln Asp Gly Asn ThrSer Thr Cys Trp Thr Pro Val 1 5 10 88 13 PRT hepatitis C virus 88 ValMet Thr Gly Asn Val Ser Arg Cys Trp Val Gln Ile 1 5 10 89 10 PRThepatitis C virus 89 Val Arg Tyr Val Gly Ala Thr Thr Ala Ser 1 5 10 9010 PRT hepatitis C virus 90 Ala Pro Ser Leu Gly Ala Val Thr Ala Pro 1 510 91 10 PRT hepatitis C virus 91 Arg Pro Arg Arg His Gln Thr Val GlnThr 1 5 10 92 10 PRT hepatitis C virus 92 Arg Pro Arg Gln His Ala ThrVal Gln Asn 1 5 10 93 9 PRT hepatitis C virus 93 Gln Pro Thr Gly Arg SerTrp Gly Gln 1 5 94 8 PRT hepatitis C virus 94 Val Gln Asp Gly Asn ThrSer Thr 1 5 95 8 PRT hepatitis C virus 95 Val Gln Asp Gly Asn Thr SerAla 1 5 96 10 PRT hepatitis C virus 96 Val Lys Tyr Val Gly Ala Thr ThrAla Ser 1 5 10 97 20 PRT hepatitis C virus 97 Leu Gly Gly Lys Pro AlaIle Val Pro Asp Lys Glu Val Leu Tyr Gln 1 5 10 15 Gln Tyr Asp Glu 20 9820 PRT hepatitis C virus 98 Leu Gly Gly Lys Pro Ala Leu Val Pro Asp LysGlu Val Leu Tyr Gln 1 5 10 15 Gln Tyr Asp Glu 20 99 20 PRT hepatitis Cvirus 99 Ser Gln Ala Ala Pro Tyr Ile Glu Gln Ala Gln Val Ile Ala His Gln1 5 10 15 Phe Lys Glu Lys 20 100 20 PRT hepatitis C virus 100 Ile AlaHis Gln Phe Lys Glu Lys Val Leu Gly Leu Leu Gln Arg Ala 1 5 10 15 ThrGln Gln Gln 20 101 20 PRT hepatitis C virus 101 Ile Ala His Gln Phe LysGlu Lys Ile Leu Gly Leu Leu Gln Arg Ala 1 5 10 15 Thr Gln Gln Gln 20 10220 PRT hepatitis C virus 102 Leu Ser Gly Lys Pro Ala Ile Ile Pro Asp ArgGlu Ala Leu Tyr Gln 1 5 10 15 Gln Phe Asp Glu 20 103 20 PRT hepatitis Cvirus 103 Leu Ser Gly Lys Pro Ala Ile Ile Pro Asp Arg Glu Val Leu TyrGln 1 5 10 15 Gln Phe Asp Glu 20 104 20 PRT hepatitis C virus 104 SerAla Ser Leu Pro Tyr Met Asp Glu Thr Arg Ala Ile Ala Gly Gln 1 5 10 15Phe Lys Glu Lys 20 105 20 PRT hepatitis C virus 105 Ile Ala Gly Gln PheLys Glu Lys Val Leu Gly Phe Ile Ser Thr Thr 1 5 10 15 Gly Gln Lys Ala 20106 340 DNA hepatitis C virus 106 ctccactgta accgaaaagg acatcagggtcgaggaggag gtctatcagt gttgtgacct 60 ggagcccgaa gcccgcaagg caattaccgccctaacagag agactctacg tgggcggtcc 120 catgcataac agcaagggag acctgtgcgggtatcgcaga tgtcgcgcaa gcggcgtcta 180 caccaccagc ttcgggaaca cactgacgtgctacctcaaa gcctcagccg ctatcaaagc 240 ggcggggctg agagactgca ccatgttggtctgtggtgat gacctggttg tcatcgctga 300 gagcgatggc gtagaggagg acaaacgacccctcggagcc 340 107 113 PRT hepatitis C virus 107 Ser Thr Val Thr Glu LysAsp Ile Arg Val Glu Glu Glu Val Tyr Gln 1 5 10 15 Cys Cys Asp Leu GluPro Glu Ala Arg Lys Ala Ile Thr Ala Leu Thr 20 25 30 Glu Arg Leu Tyr ValGly Gly Pro Met His Asn Ser Lys Gly Asp Leu 35 40 45 Cys Gly Tyr Arg ArgCys Arg Ala Ser Gly Val Tyr Thr Thr Ser Phe 50 55 60 Gly Asn Thr Leu ThrCys Tyr Leu Lys Ala Ser Ala Ala Ile Lys Ala 65 70 75 80 Ala Gly Leu ArgAsp Cys Thr Met Leu Val Cys Gly Asp Asp Leu Val 85 90 95 Val Ile Ala GluSer Asp Gly Val Glu Glu Asp Lys Arg Pro Leu Gly 100 105 110 Ala 108 340DNA hepatitis C virus 108 ctccactgta accgaaaagg acatcagggt cgaggaggaggtatatcagt gttgtgacct 60 ggagcccgag gcccgcagag caattaccgc cctaacagagagactctacg tgggcggtcc 120 catgcataac agcaggggag acctgtgcgg gtatcgcagatgccgtgcga gcggcgtcta 180 caccaccagc ttcgggaaca cactgacgtg ctatctcaaagcctcagccg ctatcagagc 240 ggcggggctg agagactgca ccatgttggt ctgtggtgatgacctggtcg tcattgctga 300 aagcgatggc gtagaggagg acaaacgagc cctcggagcc340 109 113 PRT hepatitis C virus 109 Ser Thr Val Thr Glu Lys Asp IleArg Val Glu Glu Glu Val Tyr Gln 1 5 10 15 Cys Cys Asp Leu Glu Pro GluAla Arg Arg Ala Ile Thr Ala Leu Thr 20 25 30 Glu Arg Leu Tyr Val Gly GlyPro Met His Asn Ser Arg Gly Asp Leu 35 40 45 Cys Gly Tyr Arg Arg Cys ArgAla Ser Gly Val Tyr Thr Thr Ser Phe 50 55 60 Gly Asn Thr Leu Thr Cys TyrLeu Lys Ala Ser Ala Ala Ile Arg Ala 65 70 75 80 Ala Gly Leu Arg Asp CysThr Met Leu Val Cys Gly Asp Asp Leu Val 85 90 95 Val Ile Ala Glu Ser AspGly Val Glu Glu Asp Lys Arg Ala Leu Gly 100 105 110 Ala 110 340 DNAhepatitis C virus 110 ctccactgta accgaaaaag acatcagggt cgaggaggaggtatatcagt gttgtgacct 60 ggagcccgaa gcccgcaagg taattaccgc cctaacagagagactctatg tgggcggtcc 120 catgcataat agcaaaggag acctgtgcgg gtatcgcagatgccgcgcaa gcggcgtcta 180 caccaccagc ttcgggaaca cactgacgtg ctatctcaaagcctcagccg ccatcagggc 240 gtcagggctg agagactgca ctatgctggt ctatggtgacgacctggtcg tcattgccga 300 gagcgatggc gtagaggagg acaaacgagc cctcggagtc340 111 113 PRT hepatitis C virus 111 Ser Thr Val Thr Glu Lys Asp IleArg Val Glu Glu Glu Val Tyr Gln 1 5 10 15 Cys Cys Asp Leu Glu Pro GluAla Arg Lys Val Ile Thr Ala Leu Thr 20 25 30 Glu Arg Leu Tyr Val Gly GlyPro Met His Asn Ser Lys Gly Asp Leu 35 40 45 Cys Gly Tyr Arg Arg Cys ArgAla Ser Gly Val Tyr Thr Thr Ser Phe 50 55 60 Gly Asn Thr Leu Thr Cys TyrLeu Lys Ala Ser Ala Ala Ile Arg Ala 65 70 75 80 Ser Gly Leu Arg Asp CysThr Met Leu Val Tyr Gly Asp Asp Leu Val 85 90 95 Val Ile Ala Glu Ser AspGly Val Glu Glu Asp Lys Arg Ala Leu Gly 100 105 110 Val 112 340 DNAhepatitis C virus 112 ctccactgta accgaaaagg acatcagggt cgaggaggaggtgtatcagt gttgtgacct 60 ggagcccgag gcccgcaagg caattactgc cctaacagagagactctatg tgggcggtcc 120 catgcataac agcaagggag acctgtgtgg gtatcgcagatgccgcgcaa gcggcgtcta 180 caccaccagc ttcgggaaca cactgacgtg ctacctcaaagcctcagccg ctatcagagc 240 ggcggggctg agagactgca ccatgttggt ctgtggtgatgacctggtcg tcatcgctga 300 gagcgatggc gttgaggagg acaaacgagc cctcggagcc340 113 113 PRT hepatitis C virus 113 Ser Thr Val Thr Glu Lys Asp IleArg Val Glu Glu Glu Val Tyr Gln 1 5 10 15 Cys Cys Asp Leu Glu Pro GluAla Arg Lys Ala Ile Thr Ala Leu Thr 20 25 30 Glu Arg Leu Tyr Val Gly GlyPro Met His Asn Ser Lys Gly Asp Leu 35 40 45 Cys Gly Tyr Arg Arg Cys ArgAla Ser Gly Val Tyr Thr Thr Ser Phe 50 55 60 Gly Asn Thr Leu Thr Cys TyrLeu Lys Ala Ser Ala Ala Ile Arg Ala 65 70 75 80 Ala Gly Leu Arg Asp CysThr Met Leu Val Cys Gly Asp Asp Leu Val 85 90 95 Val Ile Ala Glu Ser AspGly Val Glu Glu Asp Lys Arg Ala Leu Gly 100 105 110 Ala 114 340 DNAhepatitis C virus 114 ctccacggtg accgaaaggg atatcaggac cgaggaagagatctaccagt gctgcgacct 60 ggagcccgaa gcccgcaagg tgatatccgc cctaacggaaagactctacg tgggcggtcc 120 catgtacaac tccaaggggg acctatgcgg gcaacggaggtgccgcgcaa gcggggtcta 180 caccaccagc ttcgggaaca ctgtaacgtg ttatctcaaggccgttgcgg ctactagggc 240 cgcaggtctg aaaggttgca gcatgctggt ttgtggagacgacttagtcg tcatctgcga 300 gagcggcggc gtagaggagg atgcaagagc cctccgagcc340 115 113 PRT hepatitis C virus 115 Ser Thr Val Thr Glu Arg Asp IleArg Thr Glu Glu Glu Ile Tyr Gln 1 5 10 15 Cys Cys Asp Leu Glu Pro GluAla Arg Lys Val Ile Ser Ala Leu Thr 20 25 30 Glu Arg Leu Tyr Val Gly GlyPro Met Tyr Asn Ser Lys Gly Asp Leu 35 40 45 Cys Gly Gln Arg Arg Cys ArgAla Ser Gly Val Tyr Thr Thr Ser Phe 50 55 60 Gly Asn Thr Val Thr Cys TyrLeu Lys Ala Val Ala Ala Thr Arg Ala 65 70 75 80 Ala Gly Leu Lys Gly CysSer Met Leu Val Cys Gly Asp Asp Leu Val 85 90 95 Val Ile Cys Glu Ser GlyGly Val Glu Glu Asp Ala Arg Ala Leu Arg 100 105 110 Ala 116 340 DNAhepatitis C virus 116 ctccactgtg actgagagag acatcaaggt cgaagaagaagtctatcagt gttgtgatct 60 ggagcccgag gcccgcaagg taatagccgc cctcacggagagactctacg tgggcggccc 120 catgcataac agcaagggag acctttgcgg gtatcgtagatgccgcgcga gcggcgtata 180 caccaccagc ttcgggaaca caatgacgtg ctaccttaaggcctcagcag ccatcagggc 240 tgcggggcta aaggattgca ccatgctggt ttgcggtgacgacctagtcg tgatcgccga 300 gagcggtggc gttgaggagg acaaacgagc cctcggagct340 117 113 PRT hepatitis C virus 117 Ser Thr Val Thr Glu Arg Asp IleLys Val Glu Glu Glu Val Tyr Gln 1 5 10 15 Cys Cys Asp Leu Glu Pro GluAla Arg Lys Val Ile Ala Ala Leu Thr 20 25 30 Glu Arg Leu Tyr Val Gly GlyPro Met His Asn Ser Lys Gly Asp Leu 35 40 45 Cys Gly Tyr Arg Arg Cys ArgAla Ser Gly Val Tyr Thr Thr Ser Phe 50 55 60 Gly Asn Thr Met Thr Cys TyrLeu Lys Ala Ser Ala Ala Ile Arg Ala 65 70 75 80 Ala Gly Leu Lys Asp CysThr Met Leu Val Cys Gly Asp Asp Leu Val 85 90 95 Val Ile Ala Glu Ser GlyGly Val Glu Glu Asp Lys Arg Ala Leu Gly 100 105 110 Ala 118 574 DNAhepatitis C virus 118 acttgcggct ttgccgacct catgggatac atcccgctcgtaggcgcccc tgtgggtggc 60 gtcgccaggg ccctggcaca cggtgttagg gctgtggaggacgggatcaa ttatgcgaca 120 gggaatcttc ccggttgctc tttctctatc ttcctcttggcacttctttc gtgcctgact 180 gttcccacct cggccgtcaa ctatcgcaat gcctcgggcatctatcacat caccaatgac 240 tgcccgaact cgagcatagt gtacgagacc gagcaccacatcctacacct cccagggtgt 300 ttaccctgcg tgagggttgg gaatcagtca cgctgctgggtggccctcac tcccaccgtg 360 gcggcgcctt acatcggcgc tccgcttgaa tccctccggagtcatgtgga tctgatggta 420 ggtgccgcta ctgcgtgctc cgctctttac atcggagacctgtgcggtgg cgtattcttg 480 gttggtcaga tgttctcttt ccagccgcgg cgccactggactacgcagga ctgcaattgt 540 tccatctacg cggggcacgt tacgggccac agga 574 119191 PRT hepatitis C virus 119 Thr Cys Gly Phe Ala Asp Leu Met Gly TyrIle Pro Leu Val Gly Ala 1 5 10 15 Pro Val Gly Gly Val Ala Arg Ala LeuAla His Gly Val Arg Ala Val 20 25 30 Glu Asp Gly Ile Asn Tyr Ala Thr GlyAsn Leu Pro Gly Cys Ser Phe 35 40 45 Ser Ile Phe Leu Leu Ala Leu Leu SerCys Leu Thr Val Pro Thr Ser 50 55 60 Ala Val Asn Tyr Arg Asn Ala Ser GlyIle Tyr His Ile Thr Asn Asp 65 70 75 80 Cys Pro Asn Ser Ser Ile Val TyrGlu Thr Glu His His Ile Leu His 85 90 95 Leu Pro Gly Cys Leu Pro Cys ValArg Val Gly Asn Gln Ser Arg Cys 100 105 110 Trp Val Ala Leu Thr Pro ThrVal Ala Ala Pro Tyr Ile Gly Ala Pro 115 120 125 Leu Glu Ser Leu Arg SerHis Val Asp Leu Met Val Gly Ala Ala Thr 130 135 140 Ala Cys Ser Ala LeuTyr Ile Gly Asp Leu Cys Gly Gly Val Phe Leu 145 150 155 160 Val Gly GlnMet Phe Ser Phe Gln Pro Arg Arg His Trp Thr Thr Gln 165 170 175 Asp CysAsn Cys Ser Ile Tyr Ala Gly His Val Thr Gly His Arg 180 185 190 120 574DNA hepatitis C virus 120 acgtgcggct ttgccgacct catgggatac atcccgctcgtgggcgcccc tgtgggtggc 60 gtcgccaggg ccttggcaca tggtgtcagg gccgtggaggacgggattaa ctatgcaaca 120 gggaatcttc ccggttgctc cttttctatc ttccttctagcacttctctc gtgcttgact 180 gtcccggcct cggcgcagca ctaccggaac atctcgggcatttatcacgt caccaatgac 240 tgcccgaact ctagtatagt gtatgaagct gaccatcatatcatgcatct accagggtgt 300 gtgccttgcg tgagaaccgg gaacacctcg cgctgctgggttcctttaac acccactgtg 360 gctgccccct atgttggcgc gccgctcgaa tccatgcggcggcacgtgga cttaatggtg 420 ggtgccgcca ccgtctgctc ggccctgtac atcggagacctttgcggagg tgtcttcctg 480 gtcgggcaga tgttcacctt ccggccgcgc cgccattggactacccagga ctgcaactgc 540 tctatctatg atggccacat caccggccat agaa 574 121191 PRT hepatitis C virus 121 Thr Cys Gly Phe Ala Asp Leu Met Gly TyrIle Pro Leu Val Gly Ala 1 5 10 15 Pro Val Gly Gly Val Ala Arg Ala LeuAla His Gly Val Arg Ala Val 20 25 30 Glu Asp Gly Ile Asn Tyr Ala Thr GlyAsn Leu Pro Gly Cys Ser Phe 35 40 45 Ser Ile Phe Leu Leu Ala Leu Leu SerCys Leu Thr Val Pro Ala Ser 50 55 60 Ala Gln His Tyr Arg Asn Ile Ser GlyIle Tyr His Val Thr Asn Asp 65 70 75 80 Cys Pro Asn Ser Ser Ile Val TyrGlu Ala Asp His His Ile Met His 85 90 95 Leu Pro Gly Cys Val Pro Cys ValArg Thr Gly Asn Thr Ser Arg Cys 100 105 110 Trp Val Pro Leu Thr Pro ThrVal Ala Ala Pro Tyr Val Gly Ala Pro 115 120 125 Leu Glu Ser Met Arg ArgHis Val Asp Leu Met Val Gly Ala Ala Thr 130 135 140 Val Cys Ser Ala LeuTyr Ile Gly Asp Leu Cys Gly Gly Val Phe Leu 145 150 155 160 Val Gly GlnMet Phe Thr Phe Arg Pro Arg Arg His Trp Thr Thr Gln 165 170 175 Asp CysAsn Cys Ser Ile Tyr Asp Gly His Ile Thr Gly His Arg 180 185 190 122 574DNA hepatitis C virus 122 acgtgcggct tcgccgacct catgggatac atcccgctcgtgggcgcccc cgttgggggc 60 gtcgccaggg ccctggcgca tggcgtcagg gctgtggaggacgggattaa ctatgcgaca 120 gggaatcttc ccggttgctc tttctctatc ttcctcctggcacttctttc gtgcctcact 180 gtcccagcgt cagctgagca ctaccggaat gcttcgggcatctatcacat caccaatgac 240 tgtccgaatt ccagcgtagt ctatgaaact gaccaccatatattgcactt gccggggtgc 300 gtaccctgcg tgagggccgg gaacgtgtct cgttgctggacgccggtaac acctacggtg 360 gctgccgtat ccatggacgc tccgctcgag tccttccggcggcatgtgga cctaatggta 420 ggtgcggcca ccgtgtgttc tgtcctctat gttggagacctctgtggagg tgctttccta 480 gtggggcaga tgttcacctt ccagccgcgt cgccactggaccacgcagga ttgtaattgc 540 tccatctata ctggccatat caccggccac agga 574 123191 PRT hepatitis C virus 123 Thr Cys Gly Phe Ala Asp Leu Met Gly TyrIle Pro Leu Val Gly Ala 1 5 10 15 Pro Val Gly Gly Val Ala Arg Ala LeuAla His Gly Val Arg Ala Val 20 25 30 Glu Asp Gly Ile Asn Tyr Ala Thr GlyAsn Leu Pro Gly Cys Ser Phe 35 40 45 Ser Ile Phe Leu Leu Ala Leu Leu SerCys Leu Thr Val Pro Ala Ser 50 55 60 Ala Glu His Tyr Arg Asn Ala Ser GlyIle Tyr His Ile Thr Asn Asp 65 70 75 80 Cys Pro Asn Ser Ser Val Val TyrGlu Thr Asp His His Ile Leu His 85 90 95 Leu Pro Gly Cys Val Pro Cys ValArg Ala Gly Asn Val Ser Arg Cys 100 105 110 Trp Thr Pro Val Thr Pro ThrVal Ala Ala Val Ser Met Asp Ala Pro 115 120 125 Leu Glu Ser Phe Arg ArgHis Val Asp Leu Met Val Gly Ala Ala Thr 130 135 140 Val Cys Ser Val LeuTyr Val Gly Asp Leu Cys Gly Gly Ala Phe Leu 145 150 155 160 Val Gly GlnMet Phe Thr Phe Gln Pro Arg Arg His Trp Thr Thr Gln 165 170 175 Asp CysAsn Cys Ser Ile Tyr Thr Gly His Ile Thr Gly His Arg 180 185 190 124 31DNA artificial misc_feature HCPr206 124 tggggatccc gtatgatacc cgctgctttga 31 125 30 DNA artificial misc_feature HCPr207 125 ggcggaattcctggtcatag cctccgtgaa 30 126 12 PRT hepatitis C virus 126 Val Asn TyrArg Asn Ala Ser Gly Ile Tyr His Ile 1 5 10 127 12 PRT hepatitis C virus127 Gln His Tyr Arg Asn Ile Ser Gly Ile Tyr His Val 1 5 10 128 12 PRThepatitis C virus 128 Glu His Tyr Arg Asn Ala Ser Gly Ile Tyr His Ile 15 10 129 11 PRT hepatitis C virus 129 Val Tyr Glu Thr Glu His His IleLeu His Leu 1 5 10 130 11 PRT hepatitis C virus 130 Val Tyr Glu Ala AspHis His Ile Met His Leu 1 5 10 131 11 PRT hepatitis C virus 131 Val TyrGlu Thr Asp His His Ile Leu His Leu 1 5 10 132 13 PRT hepatitis C virus132 Val Arg Val Gly Asn Gln Ser Arg Cys Trp Val Ala Leu 1 5 10 133 13PRT hepatitis C virus 133 Val Arg Thr Gly Asn Thr Ser Arg Cys Trp ValPro Leu 1 5 10 134 13 PRT hepatitis C virus 134 Val Arg Ala Gly Asn ValSer Arg Cys Trp Thr Pro Val 1 5 10 135 10 PRT hepatitis C virus 135 AlaPro Tyr Ile Gly Ala Pro Leu Glu Ser 1 5 10 136 10 PRT hepatitis C virus136 Ala Pro Tyr Val Gly Ala Pro Leu Glu Ser 1 5 10 137 10 PRT hepatitisC virus 137 Ala Val Ser Met Asp Ala Pro Leu Glu Ser 1 5 10 138 10 PRThepatitis C virus 138 Gln Pro Arg Arg His Trp Thr Thr Gln Asp 1 5 10 13910 PRT hepatitis C virus 139 Arg Pro Arg Arg His Trp Thr Thr Gln Asp 1 510 140 10 PRT hepatitis C virus 140 Arg Pro Arg Arg His Trp Thr Thr GlnAsp 1 5 10 141 23 DNA artificial misc_feature HCPr109 141 tgggatatgatgatgaactg gtc 23 142 24 DNA artificial misc_feature HCPr14 142ccaggtacaa ccgaaccaat tgcc 24 143 957 DNA hepatitis C virus 143atgagcacaa atcctaaacc tcaaagaaaa accaaaagaa acactaaccg ccgcccacag 60gacgtcaagt tcccgggcgg tggccagatc gttggtggag tatacttgtt gccgcgcagg 120ggcccccggt tgggtgtgcg cgcgacgagg aaaacttccg agcggtccca gccacgtggg 180aggcgccagc ccatccccaa agatcggcgc cccactggca agtcctgggg aaaaccagga 240tacccttggc ccctgtacgg gaatgagggc ctcggctggg cagggtggct cctgtccccc 300cgagggtctc gcccgtcatg gggcccaact gacccccggc acaggtcacg caacttgggt 360aaggtcatcg atacccttac gtgtggcttt gccgacctca tggggtacat ccctgtcgtc 420ggcgccccag ttggtggtgt cgccagagct ctcgcgcatg gcgtgagagt tctggaagac 480gggataaact atgcaacagg gaacttgccc ggttgctcct tttctatctt cttattggcc 540ctgctatctt gtatcactgt gccggtctcc ggcttgcagg tcaagaacac cagcagctct 600tacatggtaa ccaatgactg ccagaacagt agcatcgtct ggcagctcag ggatgctgtt 660cttcacgtcc ccgggtgtgt cccttgtgag gagaagggca acatatcccg ctgttggata 720ccggtttcgc ccaatatagc tgtgagccaa cctggtgcgc ttaccaaggg cctgcggacg 780catattgata ccatcattgc atccgctacg ttttgctctg ccctgtacat aggagacctg 840tgtggcgcgg tgatgttggc ttctcaagtc ttcatcatct cgccccagca tcataagttt 900gtccaggact gcaactgttc catataccca ggccacatca ctggacatcg gatggcg 957 144319 PRT hepatitis C virus 144 Met Ser Thr Asn Pro Lys Pro Gln Arg LysThr Lys Arg Asn Thr Asn 1 5 10 15 Arg Arg Pro Gln Asp Val Lys Phe ProGly Gly Gly Gln Ile Val Gly 20 25 30 Gly Val Tyr Leu Leu Pro Arg Arg GlyPro Arg Leu Gly Val Arg Ala 35 40 45 Thr Arg Lys Thr Ser Glu Arg Ser GlnPro Arg Gly Arg Arg Gln Pro 50 55 60 Ile Pro Lys Asp Arg Arg Pro Thr GlyLys Ser Trp Gly Lys Pro Gly 65 70 75 80 Tyr Pro Trp Pro Leu Tyr Gly AsnGlu Gly Leu Gly Trp Ala Gly Trp 85 90 95 Leu Leu Ser Pro Arg Gly Ser ArgPro Ser Trp Gly Pro Thr Asp Pro 100 105 110 Arg His Arg Ser Arg Asn LeuGly Lys Val Ile Asp Thr Leu Thr Cys 115 120 125 Gly Phe Ala Asp Leu MetGly Tyr Ile Pro Val Val Gly Ala Pro Val 130 135 140 Gly Gly Val Ala ArgAla Leu Ala His Gly Val Arg Val Leu Glu Asp 145 150 155 160 Gly Ile AsnTyr Ala Thr Gly Asn Leu Pro Gly Cys Ser Phe Ser Ile 165 170 175 Phe LeuLeu Ala Leu Leu Ser Cys Ile Thr Val Pro Val Ser Gly Leu 180 185 190 GlnVal Lys Asn Thr Ser Ser Ser Tyr Met Val Thr Asn Asp Cys Gln 195 200 205Asn Ser Ser Ile Val Trp Gln Leu Arg Asp Ala Val Leu His Val Pro 210 215220 Gly Cys Val Pro Cys Glu Glu Lys Gly Asn Ile Ser Arg Cys Trp Ile 225230 235 240 Pro Val Ser Pro Asn Ile Ala Val Ser Gln Pro Gly Ala Leu ThrLys 245 250 255 Gly Leu Arg Thr His Ile Asp Thr Ile Ile Ala Ser Ala ThrPhe Cys 260 265 270 Ser Ala Leu Tyr Ile Gly Asp Leu Cys Gly Ala Val MetLeu Ala Ser 275 280 285 Gln Val Phe Ile Ile Ser Pro Gln His His Lys PheVal Gln Asp Cys 290 295 300 Asn Cys Ser Ile Tyr Pro Gly His Ile Thr GlyHis Arg Met Ala 305 310 315 145 340 DNA hepatitis C virus 145 ctcaacggtcacggagaggg acatcagaac tgaggagtcc atataccttg cttgctcttt 60 acccgagcaggcacggactg ccatacactc actgactgag aggctttacg tgggagggcc 120 catgctaaacagcaaagggc aaacctgcgg atacagacgc tgccgcgcca gcggagtgtt 180 caccactagcatgggaaata ccatcacgtg ctacgtgaag gcacaagcag cctgtaaggc 240 tgcgggcataattgccccca cgatgctggt gtgcggcgac gatctagttg tcatctcaga 300 gagtcaggggaccgaggagg acgagcggaa cctacgagcc 340 146 113 PRT hepatitis C virus 146Ser Thr Val Thr Glu Arg Asp Ile Arg Thr Glu Glu Ser Ile Tyr Leu 1 5 1015 Ala Cys Ser Leu Pro Glu Gln Ala Arg Thr Ala Ile His Ser Leu Thr 20 2530 Glu Arg Leu Tyr Val Gly Gly Pro Met Leu Asn Ser Lys Gly Gln Thr 35 4045 Cys Gly Tyr Arg Arg Cys Arg Ala Ser Gly Val Phe Thr Thr Ser Met 50 5560 Gly Asn Thr Ile Thr Cys Tyr Val Lys Ala Gln Ala Ala Cys Lys Ala 65 7075 80 Ala Gly Ile Ile Ala Pro Thr Met Leu Val Cys Gly Asp Asp Leu Val 8590 95 Val Ile Ser Glu Ser Gln Gly Thr Glu Glu Asp Glu Arg Asn Leu Arg100 105 110 Ala 147 345 DNA hepatitis C virus 147 atgagcacac ttcctaaaccacaaagaaaa accaaaagaa acaccaaccc cggccacagg 60 acgttaagtt cccaggcggcggtcagatcg ttggtggagt ttacgtgcta ccacgcaggg 120 gcccccagtt gggtgtgcgtgcagtgcgca agacttccga gcggtcgcaa cctcgcagta 180 ggcgccaacc catccccagggcgcgccgaa ccgagggcag gtcctgggct cagcccgggt 240 acccttggcc cctatatgggaatgagggct gcgggtgggc agggtggctc ctgtccccgc 300 gcggctctcg cccgtcgtggggcccaaatg acccccggcg cagga 345 148 115 PRT hepatitis C virus 148 MetSer Thr Leu Pro Lys Pro Gln Arg Lys Thr Lys Arg Asn Thr Asn 1 5 10 15Pro Gly His Arg Thr Leu Ser Ser Gln Ala Ala Val Arg Ser Leu Val 20 25 30Glu Phe Thr Cys Tyr His Ala Gly Ala Pro Ser Trp Val Cys Val Gln 35 40 45Cys Ala Arg Leu Pro Ser Gly Arg Asn Leu Ala Val Gly Ala Asn Pro 50 55 60Ser Pro Gly Arg Ala Glu Pro Arg Ala Gly Pro Gly Leu Ser Pro Gly 65 70 7580 Thr Leu Gly Pro Tyr Met Gly Met Arg Ala Ala Gly Gly Gln Gly Gly 85 9095 Ser Cys Pro Arg Ala Ala Leu Ala Arg Arg Gly Ala Gln Met Thr Pro 100105 110 Gly Ala Gly 115 149 280 DNA hepatitis C virus 149 ggcctgtgacctcaaggacg aggctaggag ggtgataact tcactcacgg agcggcttta 60 ctgtggtggtcctatgttca acagcaaggg acaacactgc ggttaccgcc gctgccgtgc 120 tagtggggtgctacccacca gcttcgggaa cacaatcacc tgttacatca aagcaaaggc 180 agctaccaaagctgccggaa ttaaaaatcc atcattcctt gtctgcggag atgacttggt 240 cgtgattgctgagagtgcag ggatcgatga ggacagagcg 280 150 93 PRT hepatitis C virus 150Ala Cys Asp Leu Lys Asp Glu Ala Arg Arg Val Ile Thr Ser Leu Thr 1 5 1015 Glu Arg Leu Tyr Cys Gly Gly Pro Met Phe Asn Ser Lys Gly Gln His 20 2530 Cys Gly Tyr Arg Arg Cys Arg Ala Ser Gly Val Leu Pro Thr Ser Phe 35 4045 Gly Asn Thr Ile Thr Cys Tyr Ile Lys Ala Lys Ala Ala Thr Lys Ala 50 5560 Ala Gly Ile Lys Asn Pro Ser Phe Leu Val Cys Gly Asp Asp Leu Val 65 7075 80 Val Ile Ala Glu Ser Ala Gly Ile Asp Glu Asp Arg Ala 85 90 151 499DNA hepatitis C virus 151 atgagcacga atcctaaacc tcaaagaaaa accaaaagaaacaccaaccg tcgcccacag 60 gacgtcaagt tcccgggcgg tggtcagatc gttggcggagtttacttgtt gccgcgcagg 120 ggccctagga tgggtgtgcg cgcgactcgg aagacttcggaacggtcgca accccgtgga 180 cggcgtcagc ctattcccaa ggcgcgccag cccacgggccggtcctgggg tcaacccggg 240 tacccttggc ccctttacgc caatgagggc ctcgggtgggcagggtggct gctctcccct 300 cgaggctctc ggcctaattg gggccccaat gacccccggcgaaaatcgcg taatttgggt 360 aaggtcatcg ataccctaac gtgcggattc gccgatctcatggggtatat cccgctcgta 420 ggcggcccca ttgggggcgt cgcaagggct ctcgcacacggtgtgagggt ccttgaggac 480 ggggtaaact atgcaacag 499 152 166 PRT hepatitisC virus 152 Met Ser Thr Asn Pro Lys Pro Gln Arg Lys Thr Lys Arg Asn ThrAsn 1 5 10 15 Arg Arg Pro Gln Asp Val Lys Phe Pro Gly Gly Gly Gln IleVal Gly 20 25 30 Gly Val Tyr Leu Leu Pro Arg Arg Gly Pro Arg Met Gly ValArg Ala 35 40 45 Thr Arg Lys Thr Ser Glu Arg Ser Gln Pro Arg Gly Arg ArgGln Pro 50 55 60 Ile Pro Lys Ala Arg Gln Pro Thr Gly Arg Ser Trp Gly GlnPro Gly 65 70 75 80 Tyr Pro Trp Pro Leu Tyr Ala Asn Glu Gly Leu Gly TrpAla Gly Trp 85 90 95 Leu Leu Ser Pro Arg Gly Ser Arg Pro Asn Trp Gly ProAsn Asp Pro 100 105 110 Arg Arg Lys Ser Arg Asn Leu Gly Lys Val Ile AspThr Leu Thr Cys 115 120 125 Gly Phe Ala Asp Leu Met Gly Tyr Ile Pro LeuVal Gly Gly Pro Ile 130 135 140 Gly Gly Val Ala Arg Ala Leu Ala His GlyVal Arg Val Leu Glu Asp 145 150 155 160 Gly Val Asn Tyr Ala Thr 165 153579 DNA hepatitis C virus 153 acgtgcggat tcgccgatct catggggtacatcccgctcg taggcggccc cgttgggggc 60 gtcgcaaggg ctctcgcaca cggtgtgagggtccttgagg acggggtaaa ctatccaaca 120 gggaatttac ccggttgctc tttctctatctttattcttg ctcttctctc gtgtctgacc 180 gttccggcct ctgcagttcc ctaccgaaatgcctctggga tttatcatgt taccaatgat 240 tgcccaaact cttccatagt ctatgaggcagataacctga tcctacacgc acctggttgc 300 gtgccttgtg tcatgacagg taatgtgagtagatgctggg tccaaattac ccctacactg 360 tcagccccga gcctcggagc agtcacggctcctcttcgga gagccgttga ctacctagcg 420 ggaggggctg ccctctgctc cgcgttatacgtaggagacg cgtgtggggc actattcttg 480 gtaggccaaa tgttcaccta taggcctcgccagcacgcta cggtgcagaa ctgcaactgt 540 tccatttaca gtggccatgt taccggccaccggatggcg 579 154 193 PRT hepatitis C virus 154 Thr Cys Gly Phe Ala AspLeu Met Gly Tyr Ile Pro Leu Val Gly Gly 1 5 10 15 Pro Val Gly Gly ValAla Arg Ala Leu Ala His Gly Val Arg Val Leu 20 25 30 Glu Asp Gly Val AsnTyr Pro Thr Gly Asn Leu Pro Gly Cys Ser Phe 35 40 45 Ser Ile Phe Ile LeuAla Leu Leu Ser Cys Leu Thr Val Pro Ala Ser 50 55 60 Ala Val Pro Tyr ArgAsn Ala Ser Gly Ile Tyr His Val Thr Asn Asp 65 70 75 80 Cys Pro Asn SerSer Ile Val Tyr Glu Ala Asp Asn Leu Ile Leu His 85 90 95 Ala Pro Gly CysVal Pro Cys Val Met Thr Gly Asn Val Ser Arg Cys 100 105 110 Trp Val GlnIle Thr Pro Thr Leu Ser Ala Pro Ser Leu Gly Ala Val 115 120 125 Thr AlaPro Leu Arg Arg Ala Val Asp Tyr Leu Ala Gly Gly Ala Ala 130 135 140 LeuCys Ser Ala Leu Tyr Val Gly Asp Ala Cys Gly Ala Leu Phe Leu 145 150 155160 Val Gly Gln Met Phe Thr Tyr Arg Pro Arg Gln His Ala Thr Val Gln 165170 175 Asn Cys Asn Cys Ser Ile Tyr Ser Gly His Val Thr Gly His Arg Met180 185 190 Ala 155 579 DNA hepatitis C virus 155 acgtgcggat tcgccgacctcgtggggtac atcccgctcg taggcggccc cgttgggggc 60 gtcgcaaggg ctctcgcacatggtgtgagg gttcttgagg acggggtgaa ttatgcaaca 120 gggaatctgc ctggttgctctttctctatc ttcattcttg cacttctctc gtgcctcact 180 gtcccggcct ctgcagttccctaccgaaat gcctctggga tctatcatgt caccaatgat 240 tgcccaaact cttccatagtctatgaggca gatgatctga tcctacacgc acctggctgc 300 gtgccttgtg tcaggaaagataatgtgagt aggtgctggg tccaaattac ccccacgctg 360 tcagccccga gcttcggagcagtcacggct ccccttcgga gagccgttga ttacttggtg 420 ggaggggctg ccctctgctccgcgttatac gttggagacg cgtgtggggc actatttttg 480 gtaggccaaa tgttcacctataggcctcgc cagcatgcta cggtgcagga ctgcaactgt 540 tccatctaca gtggccacgtcaccggccat cagatggca 579 156 193 PRT hepatitis C virus 156 Thr Cys GlyPhe Ala Asp Leu Val Gly Tyr Ile Pro Leu Val Gly Gly 1 5 10 15 Pro ValGly Gly Val Ala Arg Ala Leu Ala His Gly Val Arg Val Leu 20 25 30 Glu AspGly Val Asn Tyr Ala Thr Gly Asn Leu Pro Gly Cys Ser Phe 35 40 45 Ser IlePhe Ile Leu Ala Leu Leu Ser Cys Leu Thr Val Pro Ala Ser 50 55 60 Ala ValPro Tyr Arg Asn Ala Ser Gly Ile Tyr His Val Thr Asn Asp 65 70 75 80 CysPro Asn Ser Ser Ile Val Tyr Glu Ala Asp Asp Leu Ile Leu His 85 90 95 AlaPro Gly Cys Val Pro Cys Val Arg Lys Asp Asn Val Ser Arg Cys 100 105 110Trp Val Gln Ile Thr Pro Thr Leu Ser Ala Pro Ser Phe Gly Ala Val 115 120125 Thr Ala Pro Leu Arg Arg Ala Val Asp Tyr Leu Val Gly Gly Ala Ala 130135 140 Leu Cys Ser Ala Leu Tyr Val Gly Asp Ala Cys Gly Ala Leu Phe Leu145 150 155 160 Val Gly Gln Met Phe Thr Tyr Arg Pro Arg Gln His Ala ThrVal Gln 165 170 175 Asp Cys Asn Cys Ser Ile Tyr Ser Gly His Val Thr GlyHis Gln Met 180 185 190 Ala 157 530 DNA hepatitis C virus 157 cacctacgacagctctgctg gtggcccagt tactgcggat tccccaagtg gtcattgaca 60 tcatcgcagggagccactgg ggggtcttgt ttgccgccgc atactatgca tcggtggcta 120 actggaccaaggtcgtgctg gtcttgtttc tgtttgcagg ggttgatgct actacccaga 180 tttcgggcggctccagcgcc caaacgacgt atggcatcgc ctcatttatc acccgcggcg 240 cgcagcagaaactgcagctc ataaatacca acggaagctg gcacatcaac aggaccgccc 300 ttaattgtaatgacagcctc cagactgggt tcatagccgg cctcttctac taccataagt 360 tcaactcttctggatgcccg gatcggatgg ctagctgtag ggcccttgcc acttttgacc 420 agggctggggaactatcagc tatgccaaca tatcgggtcc cagtgatgac aaaccatatt 480 gctggcactatcccccacgg ccgtgcggag tggtgccagc ccaagaggtc 530 158 176 PRT hepatitis Cvirus 158 Pro Thr Thr Ala Leu Leu Val Ala Gln Leu Leu Arg Ile Pro GlnVal 1 5 10 15 Val Ile Asp Ile Ile Ala Gly Ser His Trp Gly Val Leu PheAla Ala 20 25 30 Ala Tyr Tyr Ala Ser Val Ala Asn Trp Thr Lys Val Val LeuVal Leu 35 40 45 Phe Leu Phe Ala Gly Val Asp Ala Thr Thr Gln Ile Ser GlyGly Ser 50 55 60 Ser Ala Gln Thr Thr Tyr Gly Ile Ala Ser Phe Ile Thr ArgGly Ala 65 70 75 80 Gln Gln Lys Leu Gln Leu Ile Asn Thr Asn Gly Ser TrpHis Ile Asn 85 90 95 Arg Thr Ala Leu Asn Cys Asn Asp Ser Leu Gln Thr GlyPhe Ile Ala 100 105 110 Gly Leu Phe Tyr Tyr His Lys Phe Asn Ser Ser GlyCys Pro Asp Arg 115 120 125 Met Ala Ser Cys Arg Ala Leu Ala Thr Phe AspGln Gly Trp Gly Thr 130 135 140 Ile Ser Tyr Ala Asn Ile Ser Gly Pro SerAsp Asp Lys Pro Tyr Cys 145 150 155 160 Trp His Tyr Pro Pro Arg Pro CysGly Val Val Pro Ala Gln Glu Val 165 170 175 159 340 DNA hepatitis Cvirus 159 ctcgaccgtt accgaacatg acataatgac cgaagagtcc atttaccaatcatgtgactt 60 gcagcccgag gcacgcgcag caatacggtc actcacccaa cgcctctactgtggaggccc 120 catgtacaac agcaaggggc aacagtgtgg ttatcgcaga tgccgcgccagcggcgtttt 180 caccaccagt atgggcaaca ccatgacgtg ctacatcaag gctttagcctcctgtagagc 240 cgcaaggctc cgggactgca cgctcctggt gtgtggtgac gatcttgtggccatctgcga 300 gagccagggg acacacgagg atgaagcaag cctgagagcc 340 160 113PRT hepatitis C virus 160 Ser Thr Val Thr Glu His Asp Ile Met Thr GluGlu Ser Ile Tyr Gln 1 5 10 15 Ser Cys Asp Leu Gln Pro Glu Ala Arg AlaAla Ile Arg Ser Leu Thr 20 25 30 Gln Arg Leu Tyr Cys Gly Gly Pro Met TyrAsn Ser Lys Gly Gln Gln 35 40 45 Cys Gly Tyr Arg Arg Cys Arg Ala Ser GlyVal Phe Thr Thr Ser Met 50 55 60 Gly Asn Thr Met Thr Cys Tyr Ile Lys AlaLeu Ala Ser Cys Arg Ala 65 70 75 80 Ala Arg Leu Arg Asp Cys Thr Leu LeuVal Cys Gly Asp Asp Leu Val 85 90 95 Ala Ile Cys Glu Ser Gln Gly Thr HisGlu Asp Glu Ala Ser Leu Arg 100 105 110 Ala 161 340 DNA hepatitis Cvirus 161 ctcaaccgcc accgaacatg acatattgac tgaagagtcc atataccaatcatgtgactc 60 gcagcccgac gcacgcgcag caatacggtc actcacccaa cgcttgttctgtggaggccc 120 catgtataac agcaaggggc aacaatgtgg ttatcgcaga tgccgcgccagcggcgtctt 180 caccaccagt atgggcaaca ccatgacgtg ctacattaag gctttagcctcctgtagaac 240 cgctgggctc cgggactaca cgctcctggt gtgtggtgac gatcatgtggccatctgcga 300 gagccagggg acacacgagg atgaagcgaa cctgagagcc 340 162 113PRT hepatitis C virus 162 Ser Thr Ala Thr Glu His Asp Ile Leu Thr GluGlu Ser Ile Tyr Gln 1 5 10 15 Ser Cys Asp Ser Gln Pro Asp Ala Arg AlaAla Ile Arg Ser Leu Thr 20 25 30 Gln Arg Leu Phe Cys Gly Gly Pro Met TyrAsn Ser Lys Gly Gln Gln 35 40 45 Cys Gly Tyr Arg Arg Cys Arg Ala Ser GlyVal Phe Thr Thr Ser Met 50 55 60 Gly Asn Thr Met Thr Cys Tyr Ile Lys AlaLeu Ala Ser Cys Arg Thr 65 70 75 80 Ala Gly Leu Arg Asp Tyr Thr Leu LeuVal Cys Gly Asp Asp His Val 85 90 95 Ala Ile Cys Glu Ser Gln Gly Thr HisGlu Asp Glu Ala Asn Leu Arg 100 105 110 Ala 163 499 DNA hepatitis Cvirus 163 atgagcacga atcctaaact tcaaagaaaa accaaacgta acaccaaccgccgccccatg 60 gacgttaagt tcccgggtgg tggccagatc gttggcggag tttacttgttgccgcgcagg 120 ggccctaggt tgggtgtgcg cgcgactcgg aagacttcgg agcggtcgcaacctcgtggg 180 aggcgccaac ctatccccaa ggcgcgccga tccgagggca gatcctgggcgcagcccggg 240 tatccttggc ccctttacgg caatgagggc tgtgggtggg cagggtggctcctgtcccct 300 cgcgggtctc ggccgtcttg gggccctaat gatccccggc ggaggtcccgcaacctgggt 360 aaggtcatcg ataccctaac atgcggcttc gccgacctca tgggatacatcccgcttgta 420 ggcgcccccg tgggtggcgt cgccagagcc ctggcacacg gtgttagggctgtggaagac 480 gggatcaact acgcaacag 499 164 166 PRT hepatitis C virus164 Met Ser Thr Asn Pro Lys Leu Gln Arg Lys Thr Lys Arg Asn Thr Asn 1 510 15 Arg Arg Pro Met Asp Val Lys Phe Pro Gly Gly Gly Gln Ile Val Gly 2025 30 Gly Val Tyr Leu Leu Pro Arg Arg Gly Pro Arg Leu Gly Val Arg Ala 3540 45 Thr Arg Lys Thr Ser Glu Arg Ser Gln Pro Arg Gly Arg Arg Gln Pro 5055 60 Ile Pro Lys Ala Arg Arg Ser Glu Gly Arg Ser Trp Ala Gln Pro Gly 6570 75 80 Tyr Pro Trp Pro Leu Tyr Gly Asn Glu Gly Cys Gly Trp Ala Gly Trp85 90 95 Leu Leu Ser Pro Arg Gly Ser Arg Pro Ser Trp Gly Pro Asn Asp Pro100 105 110 Arg Arg Arg Ser Arg Asn Leu Gly Lys Val Ile Asp Thr Leu ThrCys 115 120 125 Gly Phe Ala Asp Leu Met Gly Tyr Ile Pro Leu Val Gly AlaPro Val 130 135 140 Gly Gly Val Ala Arg Ala Leu Ala His Gly Val Arg AlaVal Glu Asp 145 150 155 160 Gly Ile Asn Tyr Ala Thr 165 165 499 DNAhepatitis C virus misc_feature (306)..(306) “n” is any nucleotide 165atgagcacga atcctaaacc tcaaagaaaa accaaacgta acaccaaccg ccgccctatg 60gacgttaagt tcccaggcgg tggtcagatc gttggcggag tttacttgtt gccgcgcagg 120ggccccaggt tgggtgtgcg cgcgactcgg aagacttcgg agcggtcgca acctcgtggg 180aggcgccaac ctatccccaa ggcgcgccga accgagggca gatcctgggc gcagcccggg 240tatccttggc ccctttacgg caatgagggc tgtgggtggg cagggtggct cctgtcccct 300cgcggntctc ggncgtcttg gggccccaat gatccccggn ggagatcccg caacttgggt 360aaggtcatcg ataccctaac atgcggcttc gccgacctca tgggatacat cccgcttgta 420ggcgcccccg tgggtggcgt cgccagggcc ctggcacatg gtgttagggc tgtggaagac 480gggatcaatt atgcaacag 499 166 126 PRT hepatitis C virus MISC_FEATURE(102)..(102) “Xaa” is any amino acid 166 Met Ser Thr Asn Pro Lys Pro GlnArg Lys Thr Lys Arg Asn Thr Asn 1 5 10 15 Arg Arg Pro Met Asp Val LysPhe Pro Gly Gly Gly Gln Ile Val Gly 20 25 30 Gly Val Tyr Leu Leu Pro ArgArg Gly Pro Arg Leu Gly Val Arg Ala 35 40 45 Thr Arg Lys Thr Ser Glu ArgSer Gln Pro Arg Gly Arg Arg Gln Pro 50 55 60 Ile Pro Lys Ala Arg Arg ThrGlu Gly Arg Ser Trp Ala Gln Pro Gly 65 70 75 80 Tyr Pro Trp Pro Leu TyrGly Asn Glu Gly Cys Gly Trp Ala Gly Trp 85 90 95 Leu Leu Ser Pro Arg XaaSer Arg Xaa Ser Trp Gly Pro Asn Asp Pro 100 105 110 Arg Xaa Arg Ser ArgAsn Leu Gly Lys Val Ile Asp Thr Leu 115 120 125 167 579 DNA hepatitis Cvirus 167 acatgcggct tcgccgacct catgggatac atcccgcttg taggcgcccccgtgggtggc 60 gtcgccaggg ccctggcaca tggtgttagg gctgtggaag acgggatcaattatgcaaca 120 gggaaccttc ccggttgctc cttttctatc ttcctcttgg cgctcctctcgtgcctgact 180 gttcccacat cggccgttaa ctatcgcaat gcttcgggca tttatcacatcaccaatgac 240 tgcccgaatg caagcatagt gtacgagacc gaaaatcaca tcttacacctcccagggtgc 300 gtaccctgtg tgaggactgg gaaccagtcg cggtgttggg tggccctcactcccacagta 360 gcgtcgccat acgccggtgc tccgcttgag cccttgcggc gtcatgtggacctgatggta 420 ggtgctgcca ccatgtgttc cgccctctac atcggcgact tgtgcggtggcttattcttg 480 gtgggccaaa tgttcacctt ccaaccgcga cgtcactgga ccactcaggactgcaattgt 540 tccatctaca cgggccacat tacgggtcat cggatggca 579 168 193PRT hepatitis C virus 168 Thr Cys Gly Phe Ala Asp Leu Met Gly Tyr IlePro Leu Val Gly Ala 1 5 10 15 Pro Val Gly Gly Val Ala Arg Ala Leu AlaHis Gly Val Arg Ala Val 20 25 30 Glu Asp Gly Ile Asn Tyr Ala Thr Gly AsnLeu Pro Gly Cys Ser Phe 35 40 45 Ser Ile Phe Leu Leu Ala Leu Leu Ser CysLeu Thr Val Pro Thr Ser 50 55 60 Ala Val Asn Tyr Arg Asn Ala Ser Gly IleTyr His Ile Thr Asn Asp 65 70 75 80 Cys Pro Asn Ala Ser Ile Val Tyr GluThr Glu Asn His Ile Leu His 85 90 95 Leu Pro Gly Cys Val Pro Cys Val ArgThr Gly Asn Gln Ser Arg Cys 100 105 110 Trp Val Ala Leu Thr Pro Thr ValAla Ser Pro Tyr Ala Gly Ala Pro 115 120 125 Leu Glu Pro Leu Arg Arg HisVal Asp Leu Met Val Gly Ala Ala Thr 130 135 140 Met Cys Ser Ala Leu TyrIle Gly Asp Leu Cys Gly Gly Leu Phe Leu 145 150 155 160 Val Gly Gln MetPhe Thr Phe Gln Pro Arg Arg His Trp Thr Thr Gln 165 170 175 Asp Cys AsnCys Ser Ile Tyr Thr Gly His Ile Thr Gly His Arg Met 180 185 190 Ala 169579 DNA hepatitis C virus 169 acatgcggct tcgccgacct catgggatacatcccgcttg taggcgcccc cgtgggtggc 60 gtcgccagag ccctggcaca cggtgttagggctgtggaag acgggatcaa ctacgcaaca 120 gggaatctcc ccggttgctc cttttctatcttcctcttgg cacttctctc gtgcctcact 180 gttcccgcgt cgggcgttaa ctatcgcaatgcttcgggcg tttatcacat caccaacgac 240 tgcccgaatg cgagcatagt gtacgagaccgacaatcaca tcttacacct cccagggtgc 300 gtaccctgtg tgaagaccgg gaaccagtcgcggtgttggg tggccctcac tcccacagtg 360 gcgtcgcctt acgtcggtgc tccgctcgagcccttgcggc gccatgtgga cctgatggta 420 ggtgctgcca ccgtgtgctc cgccctctacgtcggcgacc tgtgcggtgg cttattcttg 480 gtaggccaaa tgttcacctt ccaaccgcgacgccactgga cgacccagga ctgtaattgt 540 tccatctacg cagggcatat tacgggccatcggatggct 579 170 193 PRT hepatitis C virus 170 Thr Cys Gly Phe Ala AspLeu Met Gly Tyr Ile Pro Leu Val Gly Ala 1 5 10 15 Pro Val Gly Gly ValAla Arg Ala Leu Ala His Gly Val Arg Ala Val 20 25 30 Glu Asp Gly Ile AsnTyr Ala Thr Gly Asn Leu Pro Gly Cys Ser Phe 35 40 45 Ser Ile Phe Leu LeuAla Leu Leu Ser Cys Leu Thr Val Pro Ala Ser 50 55 60 Gly Val Asn Tyr ArgAsn Ala Ser Gly Val Tyr His Ile Thr Asn Asp 65 70 75 80 Cys Pro Asn AlaSer Ile Val Tyr Glu Thr Asp Asn His Ile Leu His 85 90 95 Leu Pro Gly CysVal Pro Cys Val Lys Thr Gly Asn Gln Ser Arg Cys 100 105 110 Trp Val AlaLeu Thr Pro Thr Val Ala Ser Pro Tyr Val Gly Ala Pro 115 120 125 Leu GluPro Leu Arg Arg His Val Asp Leu Met Val Gly Ala Ala Thr 130 135 140 ValCys Ser Ala Leu Tyr Val Gly Asp Leu Cys Gly Gly Leu Phe Leu 145 150 155160 Val Gly Gln Met Phe Thr Phe Gln Pro Arg Arg His Trp Thr Thr Gln 165170 175 Asp Cys Asn Cys Ser Ile Tyr Ala Gly His Ile Thr Gly His Arg Met180 185 190 Ala 171 579 DNA hepatitis C virus 171 acatgcggct tcgccgacctcatgggatac atcccgcttg tgggcgcccc tgttggtggc 60 gtcgccagag cccttgcgcacggcgtcagg gctgtggaag acgggattaa ctatgcaaca 120 gggaaccttc ctggttgctccttttctatc ttccttctgg cacttctctc gtgcctgact 180 gtccccgcct cggctgtgcattatcacaac acctcgggca tctaccacct caccaatgac 240 tgccctaact ctagcatagtctttgaggca gtccatcaca tcttgcacct tccaggatgc 300 gtcccttgtg taagaactgggaaccagtct cggtgctggg tagccttgac ccccacgctg 360 gccgcgccat accttggcgctccactcgag tccatgcggc gtcacgtgga tttgatggtg 420 ggcactgcta cattgtgctcagcactctac gttggggacc tgtgcggggg catattccta 480 gcgggccaga tgttcaccttccggccccgc ctccattgga ccacccagga gtgcaattgt 540 tccacctatc cgggccacatcacgggtcat agaatggcg 579 172 193 PRT hepatitis C virus 172 Thr Cys GlyPhe Ala Asp Leu Met Gly Tyr Ile Pro Leu Val Gly Ala 1 5 10 15 Pro ValGly Gly Val Ala Arg Ala Leu Ala His Gly Val Arg Ala Val 20 25 30 Glu AspGly Ile Asn Tyr Ala Thr Gly Asn Leu Pro Gly Cys Ser Phe 35 40 45 Ser IlePhe Leu Leu Ala Leu Leu Ser Cys Leu Thr Val Pro Ala Ser 50 55 60 Ala ValHis Tyr His Asn Thr Ser Gly Ile Tyr His Leu Thr Asn Asp 65 70 75 80 CysPro Asn Ser Ser Ile Val Phe Glu Ala Val His His Ile Leu His 85 90 95 LeuPro Gly Cys Val Pro Cys Val Arg Thr Gly Asn Gln Ser Arg Cys 100 105 110Trp Val Ala Leu Thr Pro Thr Leu Ala Ala Pro Tyr Leu Gly Ala Pro 115 120125 Leu Glu Ser Met Arg Arg His Val Asp Leu Met Val Gly Thr Ala Thr 130135 140 Leu Cys Ser Ala Leu Tyr Val Gly Asp Leu Cys Gly Gly Ile Phe Leu145 150 155 160 Ala Gly Gln Met Phe Thr Phe Arg Pro Arg Leu His Trp ThrThr Gln 165 170 175 Glu Cys Asn Cys Ser Thr Tyr Pro Gly His Ile Thr GlyHis Arg Met 180 185 190 Ala 173 579 DNA hepatitis C virus 173 acgtgcggttccgccgacct catgggatac atcccgctcg taggcgcccc tgtgggtggc 60 gtcgccagggccttggcgca tggcgtcagg gctgtggagg acgggataaa ctatgcaaca 120 gggaaccttcctggttgctc tttttctatc ttccttctgg cacttctctc gtgcctgact 180 gtccccgcctcagctgtgca ttatcacaac acctcgggca tctatcacat cactaatgac 240 tgccctaactctagcatagt ctttgaggca gagcatcaca tcttgcatct tccaggatgc 300 gtcccctgtgtgagaactgg gaaccagtca cgatgctgga tagccttgac ccctacgttg 360 gccgcgccacacattggcgc tccacttgag tccatgcgac gtcatgtgga tttgatggta 420 ggcactgccacattgtgctc cgcactctac attggagatc tgtgcggagg catatttcta 480 gtgggccagatgttcaactt caggccccgc ctgcactgga ccacccagga gtgcaattgt 540 tccatctatccaggccacat cacgggtcac agaatggcg 579 174 193 PRT hepatitis C virus 174Thr Cys Gly Ser Ala Asp Leu Met Gly Tyr Ile Pro Leu Val Gly Ala 1 5 1015 Pro Val Gly Gly Val Ala Arg Ala Leu Ala His Gly Val Arg Ala Val 20 2530 Glu Asp Gly Ile Asn Tyr Ala Thr Gly Asn Leu Pro Gly Cys Ser Phe 35 4045 Ser Ile Phe Leu Leu Ala Leu Leu Ser Cys Leu Thr Val Pro Ala Ser 50 5560 Ala Val His Tyr His Asn Thr Ser Gly Ile Tyr His Ile Thr Asn Asp 65 7075 80 Cys Pro Asn Ser Ser Ile Val Phe Glu Ala Glu His His Ile Leu His 8590 95 Leu Pro Gly Cys Val Pro Cys Val Arg Thr Gly Asn Gln Ser Arg Cys100 105 110 Trp Ile Ala Leu Thr Pro Thr Leu Ala Ala Pro His Ile Gly AlaPro 115 120 125 Leu Glu Ser Met Arg Arg His Val Asp Leu Met Val Gly ThrAla Thr 130 135 140 Leu Cys Ser Ala Leu Tyr Ile Gly Asp Leu Cys Gly GlyIle Phe Leu 145 150 155 160 Val Gly Gln Met Phe Asn Phe Arg Pro Arg LeuHis Trp Thr Thr Gln 165 170 175 Glu Cys Asn Cys Ser Ile Tyr Pro Gly HisIle Thr Gly His Arg Met 180 185 190 Ala 175 579 DNA hepatitis C virus175 acgtgcggct ttgccgacct catgggatac atcccgctcg tgggcgcccc tgtgggtggc 60gtcgccaggg ccttggcaca tggtgtcagg gccgtggagg acgggattaa ctatgcaaca 120gggaatcttc ccggttgctc cttttctatc ttccttctag cacttctctc gtgcttgact 180gtcccggcct cggcgcagca ctaccggaac atctcgggca tttatcacgt caccaatgac 240tgcccgaact ctagtatagt gtatgaagct gaccatcata tcatgcatct accagggtgt 300gtgccttgcg tgagaaccgg gaacacctcg cgctgctggg ttcctttaac acccactgtg 360gctgccccct atgttggcgc gccgctcgaa tccatgcggc ggcacgtgga cttaatggtg 420ggtgccgcca ccgtctgctc ggccctgtac atcggagacc tttgcggagg tgtcttcctg 480gtcgggcaga tgttcacctt ccggccgcgc cgccattgga ctacccagga ctgcaactgc 540tctatctatg atggccacat caccggccat agaatggct 579 176 193 PRT hepatitis Cvirus 176 Thr Cys Gly Phe Ala Asp Leu Met Gly Tyr Ile Pro Leu Val GlyAla 1 5 10 15 Pro Val Gly Gly Val Ala Arg Ala Leu Ala His Gly Val ArgAla Val 20 25 30 Glu Asp Gly Ile Asn Tyr Ala Thr Gly Asn Leu Pro Gly CysSer Phe 35 40 45 Ser Ile Phe Leu Leu Ala Leu Leu Ser Cys Leu Thr Val ProAla Ser 50 55 60 Ala Gln His Tyr Arg Asn Ile Ser Gly Ile Tyr His Val ThrAsn Asp 65 70 75 80 Cys Pro Asn Ser Ser Ile Val Tyr Glu Ala Asp His HisIle Met His 85 90 95 Leu Pro Gly Cys Val Pro Cys Val Arg Thr Gly Asn ThrSer Arg Cys 100 105 110 Trp Val Pro Leu Thr Pro Thr Val Ala Ala Pro TyrVal Gly Ala Pro 115 120 125 Leu Glu Ser Met Arg Arg His Val Asp Leu MetVal Gly Ala Ala Thr 130 135 140 Val Cys Ser Ala Leu Tyr Ile Gly Asp LeuCys Gly Gly Val Phe Leu 145 150 155 160 Val Gly Gln Met Phe Thr Phe ArgPro Arg Arg His Trp Thr Thr Gln 165 170 175 Asp Cys Asn Cys Ser Ile TyrAsp Gly His Ile Thr Gly His Arg Met 180 185 190 Ala 177 579 DNAhepatitis C virus 177 acgtgcgggt tcgccgacct catgggatac atcccgctcgtgggcgctcc agtaggaggc 60 gtcgccagag ccttggcgca tggcgtcagg gctgtggaggacgggatcaa ttacgcaaca 120 gggaaccttc ccggctgctc cttttctatc ttcctcttggtacttctctc gcgcctaact 180 gtcccagcgt ctgctcagca ctaccggaat gcatcgggcatctaccatgt caccaacgac 240 tgcccgaact ccagtattgt gtatgaagcc gaccatcacatcatgcacct acccgggtgt 300 gtgccctgtg taagaactgg gaatgtctcg cgttgctggattcctttaac acccactgta 360 gccgtcccct acctcggggc tccacttacg tctgtacggcagcatgtgga cctgatggtg 420 ggggcggcca ccttatgctc tgccctctac atcggagaccattgcggagg tgtcttcttg 480 gcagggcaga tggtcagttt ccaaccccgg cgtcattggactacccagga ttgcaactgt 540 tccatctatg tgggccacat caccggccac aggatggcc 579178 193 PRT hepatitis C virus 178 Thr Cys Gly Phe Ala Asp Leu Met GlyTyr Ile Pro Leu Val Gly Ala 1 5 10 15 Pro Val Gly Gly Val Ala Arg AlaLeu Ala His Gly Val Arg Ala Val 20 25 30 Glu Asp Gly Ile Asn Tyr Ala ThrGly Asn Leu Pro Gly Cys Ser Phe 35 40 45 Ser Ile Phe Leu Leu Val Leu LeuSer Arg Leu Thr Val Pro Ala Ser 50 55 60 Ala Gln His Tyr Arg Asn Ala SerGly Ile Tyr His Val Thr Asn Asp 65 70 75 80 Cys Pro Asn Ser Ser Ile ValTyr Glu Ala Asp His His Ile Met His 85 90 95 Leu Pro Gly Cys Val Pro CysVal Arg Thr Gly Asn Val Ser Arg Cys 100 105 110 Trp Ile Pro Leu Thr ProThr Val Ala Val Pro Tyr Leu Gly Ala Pro 115 120 125 Leu Thr Ser Val ArgGln His Val Asp Leu Met Val Gly Ala Ala Thr 130 135 140 Leu Cys Ser AlaLeu Tyr Ile Gly Asp His Cys Gly Gly Val Phe Leu 145 150 155 160 Ala GlyGln Met Val Ser Phe Gln Pro Arg Arg His Trp Thr Thr Gln 165 170 175 AspCys Asn Cys Ser Ile Tyr Val Gly His Ile Thr Gly His Arg Met 180 185 190Ala 179 579 DNA hepatitis C virus misc_feature (568)..(579) “n” is anynucleotide 179 acctgcggct tcgccgacct catgggatac atcccgctcg taggcgcccccgtgggaggc 60 gtcgccagar ctctggcgca tggcgtcagg gctctggaag acgggatcaattatgcaaca 120 gggaatcttc ctggttgctc tttctctatc tcccttcttg aacttctctcgtgcctgact 180 gttcccgcct cagccatcca ctatcgcaat gcttcggacg gttattatatcaccaatgat 240 tgcccgaact ctagcatagt gtatgaagcc gagaaccaca tcttgcaccttccggggtgt 300 ataccctgtg tgaagaccgg gaatcagtcg cggtgctggg tggctctcacccccacgctg 360 gcggccccac acctacgtgc tccgctttcg tccttacggg cgcatgtggacctaatggtg 420 ggggccgcca cggcatgctc cgctttttac attggagatc tgtgcgggggtgtgtttttg 480 gcgggccaac tgttcactat ccggccacgc attcatgaaa ccactcaggactgcaattgc 540 tccatctact cagggcacat cacgggtnnn nnnnnnnnn 579 180 193PRT hepatitis C virus MISC_FEATURE (24)..(24) “Xaa” is any amino acid180 Thr Cys Gly Phe Ala Asp Leu Met Gly Tyr Ile Pro Leu Val Gly Ala 1 510 15 Pro Val Gly Gly Val Ala Arg Xaa Leu Ala His Gly Val Arg Ala Leu 2025 30 Glu Asp Gly Ile Asn Tyr Ala Thr Gly Asn Leu Pro Gly Cys Ser Phe 3540 45 Ser Ile Ser Leu Leu Glu Leu Leu Ser Cys Leu Thr Val Pro Ala Ser 5055 60 Ala Ile His Tyr Arg Asn Ala Ser Asp Gly Tyr Tyr Ile Thr Asn Asp 6570 75 80 Cys Pro Asn Ser Ser Ile Val Tyr Glu Ala Glu Asn His Ile Leu His85 90 95 Leu Pro Gly Cys Ile Pro Cys Val Lys Thr Gly Asn Gln Ser Arg Cys100 105 110 Trp Val Ala Leu Thr Pro Thr Leu Ala Ala Pro His Leu Arg AlaPro 115 120 125 Leu Ser Ser Leu Arg Ala His Val Asp Leu Met Val Gly AlaAla Thr 130 135 140 Ala Cys Ser Ala Phe Tyr Ile Gly Asp Leu Cys Gly GlyVal Phe Leu 145 150 155 160 Ala Gly Gln Leu Phe Thr Ile Arg Pro Arg IleHis Glu Thr Thr Gln 165 170 175 Asp Cys Asn Cys Ser Ile Tyr Ser Gly HisIle Thr Gly Xaa Xaa Xaa 180 185 190 Xaa 181 579 DNA hepatitis C virusmisc_feature (152)..(152) “n” is any nucleotide 181 gcgtgcggcttcgccgatct catgggatac atcccgctcg taggcgcccc cgtgggtggc 60 gtcgccagagccctggcgca cggtgttagg gctgtggagg acgggattaa ctacgcaaca 120 gggaatcttcctggttgctc tttctctatc tnccttctgg cacttctctc gtgcctgact 180 gtcccggcctcggctcagca ctaccggaat gtctcgggca tctaccacgt caccaatgat 240 tgcccgaattccagcatagt gtatgaagcc gatcaccaca tcatgcactt accagggtgc 300 ataccctgcgtgaggaccgg gaacgtttcg cgctgctggg tatctctgac acctactgtg 360 gctgctccctacctcggggc tccgcttacg tcgctacggc ggcatgtgga tttgatggtg 420 ggtgcagccaccctttgctc tgccctctac gtcggagacc tctgtggagg tgtcttccta 480 gtgggacagatgttcacctt ccagccgcgc cgccactgga ccactcagga ctgcaactgc 540 tccatttacgtcggccacat cacaggccac agaatggct 579 182 193 PRT hepatitis C virusMISC_FEATURE (51)..(51) “Xaa” is any amino acid 182 Ala Cys Gly Phe AlaAsp Leu Met Gly Tyr Ile Pro Leu Val Gly Ala 1 5 10 15 Pro Val Gly GlyVal Ala Arg Ala Leu Ala His Gly Val Arg Ala Val 20 25 30 Glu Asp Gly IleAsn Tyr Ala Thr Gly Asn Leu Pro Gly Cys Ser Phe 35 40 45 Ser Ile Xaa LeuLeu Ala Leu Leu Ser Cys Leu Thr Val Pro Ala Ser 50 55 60 Ala Gln His TyrArg Asn Val Ser Gly Ile Tyr His Val Thr Asn Asp 65 70 75 80 Cys Pro AsnSer Ser Ile Val Tyr Glu Ala Asp His His Ile Met His 85 90 95 Leu Pro GlyCys Ile Pro Cys Val Arg Thr Gly Asn Val Ser Arg Cys 100 105 110 Trp ValSer Leu Thr Pro Thr Val Ala Ala Pro Tyr Leu Gly Ala Pro 115 120 125 LeuThr Ser Leu Arg Arg His Val Asp Leu Met Val Gly Ala Ala Thr 130 135 140Leu Cys Ser Ala Leu Tyr Val Gly Asp Leu Cys Gly Gly Val Phe Leu 145 150155 160 Val Gly Gln Met Phe Thr Phe Gln Pro Arg Arg His Trp Thr Thr Gln165 170 175 Asp Cys Asn Cys Ser Ile Tyr Val Gly His Ile Thr Gly His ArgMet 180 185 190 Ala 183 579 DNA hepatitis C virus 183 acctgcggctttgccgacct catgggatac atcccgctcg taggcgcccc tgtgggtggc 60 gtcgccagggccctagaaca cggtgttagg gctgtggagg acggtattaa ttatgcaaca 120 gggaatctccccggttgctc tttttctatc tccctcttgg cacttctttc gtgcctgact 180 gttcccacctcagccgtcaa ctatcgcaac gcctcgggcg tctatcatat caccaatgac 240 tgcccgaattcgagcatagt gtacgaggct gactaccaca tcctacacct ccctgggtgc 300 ttaccctgcgtgagggttgg gaatcagtca cgctgctggg tggcccttac tcccaccgtg 360 gcggcgccttacgttggtgc tccgctagaa tccctccgga gtcatgtgga tctgatggta 420 ggtgctgctactgtgtgctc cgctctttac atcggggacc tgtgcggtgg cgtatttttg 480 gttggtcagatgttttcttt ccagccgcga cgccactgga ccacgcagga ctgcaattgt 540 tctatctacgcggggcacgt tacgggccac aggatggca 579 184 193 PRT hepatitis C virus 184Thr Cys Gly Phe Ala Asp Leu Met Gly Tyr Ile Pro Leu Val Gly Ala 1 5 1015 Pro Val Gly Gly Val Ala Arg Ala Leu Ala His Gly Val Arg Ala Val 20 2530 Glu Asp Gly Ile Asn Tyr Ala Thr Gly Asn Leu Pro Gly Cys Ser Phe 35 4045 Ser Ile Phe Leu Leu Ala Leu Leu Ser Cys Leu Thr Val Pro Thr Ser 50 5560 Ala Val Asn Tyr Arg Asn Ala Ser Gly Ile Tyr His Ile Thr Asn Asp 65 7075 80 Cys Pro Asn Ala Ser Ile Val Tyr Glu Thr Glu Asn His Ile Leu His 8590 95 Leu Pro Gly Cys Val Pro Cys Val Arg Thr Gly Asn Gln Ser Arg Cys100 105 110 Trp Val Ala Leu Thr Pro Thr Val Ala Ser Pro Tyr Ala Gly AlaPro 115 120 125 Leu Glu Pro Leu Arg Arg His Val Asp Leu Met Val Gly AlaAla Thr 130 135 140 Met Cys Ser Ala Leu Tyr Ile Gly Asp Leu Cys Gly GlyLeu Phe Leu 145 150 155 160 Val Gly Gln Met Phe Thr Phe Gln Pro Arg ArgHis Trp Thr Thr Gln 165 170 175 Asp Cys Asn Cys Ser Ile Tyr Thr Gly HisIle Thr Gly His Arg Met 180 185 190 Ala 185 579 DNA hepatitis C virus185 acttgcggct ttgccgacct catgggatac atcccgctcg taggcgcccc cgtgggtggc 60gtcgccagag ccctggaaca tggtgttagg gctgtggagg acggcatcaa ttatgcaaca 120gggaatctcc ccggttgctc tttctctatc tacctcttgg cacttctctc gtgcctgact 180gttcccacct cggccatcca ctatcgcaat gcctcgggcg tctaccacgt caccaatgac 240tgcccgaact cgagcatagt gtacgaggcc gaccaccaca tcctacacct tccagggtgc 300ttaccctgtg tgagggttgg gaatcagtca cgttgttggg tggccctctc tcccaccgtg 360gcggcgcctt acatcggtgc tccagttgaa tccttccgga gacacgtgga catgatggtg 420ggcgctgcta ctgtgtgctc cgctctctat attggggact tgtgtggtgg cgtattcttg 480gttggtcaga tgttttcttt ccggccacga cgccactgga ctacgcagga ctgcaattgt 540tccatctacg cggggcacat cactggccac ggaatggca 579 186 193 PRT hepatitis Cvirus 186 Thr Cys Gly Phe Ala Asp Leu Met Gly Tyr Ile Pro Leu Val GlyAla 1 5 10 15 Pro Val Gly Gly Val Ala Arg Ala Leu Glu His Gly Val ArgAla Val 20 25 30 Glu Asp Gly Ile Asn Tyr Ala Thr Gly Asn Leu Pro Gly CysSer Phe 35 40 45 Ser Ile Tyr Leu Leu Ala Leu Leu Ser Cys Leu Thr Val ProThr Ser 50 55 60 Ala Ile His Tyr Arg Asn Ala Ser Gly Val Tyr His Val ThrAsn Asp 65 70 75 80 Cys Pro Asn Ser Ser Ile Val Tyr Glu Ala Asp His HisIle Leu His 85 90 95 Leu Pro Gly Cys Leu Pro Cys Val Arg Val Gly Asn GlnSer Arg Cys 100 105 110 Trp Val Ala Leu Ser Pro Thr Val Ala Ala Pro TyrIle Gly Ala Pro 115 120 125 Val Glu Ser Phe Arg Arg His Val Asp Met MetVal Gly Ala Ala Thr 130 135 140 Val Cys Ser Ala Leu Tyr Ile Gly Asp LeuCys Gly Gly Val Phe Leu 145 150 155 160 Val Gly Gln Met Phe Ser Phe ArgPro Arg Arg His Trp Thr Thr Gln 165 170 175 Asp Cys Asn Cys Ser Ile TyrAla Gly His Ile Thr Gly His Gly Met 180 185 190 Ala 187 579 DNAhepatitis C virus 187 acttgcggct ttgccgacct catgggatac atcccgctcgtaggcgcccc tgtgggtggc 60 gtcgccaggg ccctggcaca cggtgttagg gctgtggaggacgggatcaa ttatgcgaca 120 gggaatcttc ccggttgctc tttctctatc ttcctcttggcacttctttc gtgcctgact 180 gttcccacct cggccgtcaa ctatcgcaat gcctcgggcatctatcacat caccaatgac 240 tgcccgaact cgagcatagt gtacgagacc gagcaccacatcctacacct cccagggtgt 300 ttaccctgcg tgagggttgg gaatcagtca cgctgctgggtggccctcac tcccaccgtg 360 gcggcgcctt acatcggcgc tccgcttgaa tccctccggagtcatgtgga tctgatggta 420 ggtgccgcta ctgcgtgctc cgctctttac atcggagacctgtgcggtgg cgtatttttg 480 gttggtcaga tgttctcttt ccagccgcgg cgccactggactacgcagga ctgcaattgt 540 tccatctacg cggggcacgt tacgggccac aggatggca 579188 193 PRT hepatitis C virus 188 Thr Cys Gly Phe Ala Asp Leu Met GlyTyr Ile Pro Leu Val Gly Ala 1 5 10 15 Pro Val Gly Gly Val Ala Arg AlaLeu Ala His Gly Val Arg Ala Val 20 25 30 Glu Asp Gly Ile Asn Tyr Ala ThrGly Asn Leu Pro Gly Cys Ser Phe 35 40 45 Ser Ile Phe Leu Leu Ala Leu LeuSer Cys Leu Thr Val Pro Thr Ser 50 55 60 Ala Val Asn Tyr Arg Asn Ala SerGly Ile Tyr His Ile Thr Asn Asp 65 70 75 80 Cys Pro Asn Ser Ser Ile ValTyr Glu Thr Glu His His Ile Leu His 85 90 95 Leu Pro Gly Cys Leu Pro CysVal Arg Val Gly Asn Gln Ser Arg Cys 100 105 110 Trp Val Ala Leu Thr ProThr Val Ala Ala Pro Tyr Ile Gly Ala Pro 115 120 125 Leu Glu Ser Leu ArgSer His Val Asp Leu Met Val Gly Ala Ala Thr 130 135 140 Ala Cys Ser AlaLeu Tyr Ile Gly Asp Leu Cys Gly Gly Val Phe Leu 145 150 155 160 Val GlyGln Met Phe Ser Phe Gln Pro Arg Arg His Trp Thr Thr Gln 165 170 175 AspCys Asn Cys Ser Ile Tyr Ala Gly His Val Thr Gly His Arg Met 180 185 190Ala 189 579 DNA hepatitis C virus 189 acgtgcggct tcgccgacct catgggatacatcccgctcg tgggcgcccc cgttgggggc 60 gtcgccaggg ccctggcgca tggcgtcagggctgtggagg acgggattaa ctatgcgaca 120 gggaatcttc ccggttgctc tttctctatcttcctcctgg cacttctttc gtgcctcact 180 gtcccagcgt cagctgagca ctaccggaatgcttcgggca tctatcacat caccaatgac 240 tgtccgaatt ccagcgtagt ctatgaaactgaccaccata tattgcactt gccggggtgc 300 gtaccctgcg tgagggccgg gaacgtgtctcgttgctgga cgccggtaac acctacggtg 360 gctgccgtat ccatggacgc tccgctcgagtccttccggc ggcatgtgga cctaatggta 420 ggtgcggcca ccgtgtgttc tgtcctctatgttggagacc tctgtggagg tgctttccta 480 gtggggcaga tgttcacctt ccagccgcgtcgccactgga ccacgcagga ttgtaattgc 540 tccatctata ctggccatat caccggccacaggatggcg 579 190 193 PRT hepatitis C virus 190 Thr Cys Gly Phe Ala AspLeu Met Gly Tyr Ile Pro Leu Val Gly Ala 1 5 10 15 Pro Val Gly Gly ValAla Arg Ala Leu Ala His Gly Val Arg Ala Val 20 25 30 Glu Asp Gly Ile AsnTyr Ala Thr Gly Asn Leu Pro Gly Cys Ser Phe 35 40 45 Ser Ile Phe Leu LeuAla Leu Leu Ser Cys Leu Thr Val Pro Ala Ser 50 55 60 Ala Glu His Tyr ArgAsn Ala Ser Gly Ile Tyr His Ile Thr Asn Asp 65 70 75 80 Cys Pro Asn SerSer Val Val Tyr Glu Thr Asp His His Ile Leu His 85 90 95 Leu Pro Gly CysVal Pro Cys Val Arg Ala Gly Asn Val Ser Arg Cys 100 105 110 Trp Thr ProVal Thr Pro Thr Val Ala Ala Val Ser Met Asp Ala Pro 115 120 125 Leu GluSer Phe Arg Arg His Val Asp Leu Met Val Gly Ala Ala Thr 130 135 140 ValCys Ser Val Leu Tyr Val Gly Asp Leu Cys Gly Gly Ala Phe Leu 145 150 155160 Val Gly Gln Met Phe Thr Phe Gln Pro Arg Arg His Trp Thr Thr Gln 165170 175 Asp Cys Asn Cys Ser Ile Tyr Thr Gly His Ile Thr Gly His Arg Met180 185 190 Ala 191 289 DNA hepatitis C virus 191 atgagcacga atcctaaacctcaaagaaaa accaaacgta acaccaaccg ccgccccatg 60 gacgttaagt tcccgggcggtggccagatc gttggtggag tttacttgtt gccgcgcagg 120 ggccccaggt tgggtgtgcgcgcgactagg aagacttcgg agcggtcgca acctcgtggg 180 agacgtcagc ctatccccaaggcacgtcga tctgagggaa ggtcctgggc tcagcccggg 240 tacccatggc ctctttacggtaatgagggt tgtgggtggg caggatggg 289 192 96 PRT hepatitis C virus 192 MetSer Thr Asn Pro Lys Pro Gln Arg Lys Thr Lys Arg Asn Thr Asn 1 5 10 15Arg Arg Pro Met Asp Val Lys Phe Pro Gly Gly Gly Gln Ile Val Gly 20 25 30Gly Val Tyr Leu Leu Pro Arg Arg Gly Pro Arg Leu Gly Val Arg Ala 35 40 45Thr Arg Lys Thr Ser Glu Arg Ser Gln Pro Arg Gly Arg Arg Gln Pro 50 55 60Ile Pro Lys Ala Arg Arg Ser Glu Gly Arg Ser Trp Ala Gln Pro Gly 65 70 7580 Tyr Pro Trp Pro Leu Tyr Gly Asn Glu Gly Cys Gly Trp Ala Gly Trp 85 9095 193 498 DNA hepatitis C virus 193 atgagcacga atcctaaacc tcaaagaaaaaccaaacgta acaccaaccg ccgccctatg 60 gacgtaaagt tcccgggcgg tggacagatcgttggcggag tttacttgtt gccgcgcagg 120 ggcccccggt tgggtgtgcg cgcgactcggaagacttcgg agcggtcgca acctcgtggc 180 aggcgtcaac ctatccccaa ggcgcgccggtccgagggca ggtcctgggc gcaagccggg 240 tacccctggc ccctctatgg caatgagggctgtgggtggg cagggtggct cctgtctcct 300 cgcggctctc ggccatcttg gggcccaaatgatccccggc ggagatcgcg caatctgggt 360 aaggtcatcg ataccctgac gtgcggcttcgccgacctca tgggatacat cccgctcgtg 420 ggcgcccccg tcgggggcgt cgccagggccctggcgcatg gcgtcagggc tgtggaggac 480 gggattaact atcgacag 498 194 166 PRThepatitis C virus 194 Met Ser Thr Asn Pro Lys Pro Gln Arg Lys Thr LysArg Asn Thr Asn 1 5 10 15 Arg Arg Pro Met Asp Val Lys Phe Pro Gly GlyGly Gln Ile Val Gly 20 25 30 Gly Val Tyr Leu Leu Pro Arg Arg Gly Pro ArgLeu Gly Val Arg Ala 35 40 45 Thr Arg Lys Thr Ser Glu Arg Ser Gln Pro ArgGly Arg Arg Gln Pro 50 55 60 Ile Pro Lys Ala Arg Arg Ser Glu Gly Arg SerTrp Ala Gln Ala Gly 65 70 75 80 Tyr Pro Trp Pro Leu Tyr Gly Asn Glu GlyCys Gly Trp Ala Gly Trp 85 90 95 Leu Leu Ser Pro Arg Gly Ser Arg Pro SerTrp Gly Pro Asn Asp Pro 100 105 110 Arg Arg Arg Ser Arg Asn Leu Gly LysVal Ile Asp Thr Leu Thr Cys 115 120 125 Gly Phe Ala Asp Leu Met Gly TyrIle Pro Leu Val Gly Ala Pro Val 130 135 140 Gly Gly Val Ala Arg Ala LeuAla His Gly Val Arg Ala Val Glu Asp 145 150 155 160 Gly Ile Asn Tyr ArgGln 165 195 579 DNA hepatitis C virus 195 acgtgcggat tcgccgacctcgtggggtac atcccgctcg taggcggccc cgttgggggc 60 gtcgcaaggg ctctcgcacatggtgtgagg gttcttgagg acggggtgaa ttatgcaaca 120 gggaatctgc ctggttgctctttctctatc ttcattcttg cacttctctc gtgcctcact 180 gtcccggcct ctgcagttccctaccgaaat gcctctggga tctatcatgt caccaatgat 240 tgcccaaact cttccatagtctatgaggca gatgatctga tcctacacgc acctggctgc 300 gtgccttgtg tcaggaaagataatgtgagt aggtgctggg tccaaattac ccccacgctg 360 tcagccccga gcttcggagcagtcacggct ccccttcgga gagccgttga ttacttggtg 420 ggaggggctg ccctctgctccgcgttatac gttggagacg cgtgtggggc actatttttg 480 gtaggccaaa tgttcacctataggcctcgc cagcatgcta cggtgcagga ctgcaactgt 540 tccatctaca gtggccacgtcaccggccat cagatggca 579 196 193 PRT hepatitis C virus 196 Thr Cys GlyPhe Ala Asp Leu Val Gly Tyr Ile Pro Leu Val Gly Gly 1 5 10 15 Pro ValGly Gly Val Ala Arg Ala Leu Ala His Gly Val Arg Val Leu 20 25 30 Glu AspGly Val Asn Tyr Ala Thr Gly Asn Leu Pro Gly Cys Ser Phe 35 40 45 Ser IlePhe Ile Leu Ala Leu Leu Ser Cys Leu Thr Val Pro Ala Ser 50 55 60 Ala ValPro Tyr Arg Asn Ala Ser Gly Ile Tyr His Val Thr Asn Asp 65 70 75 80 CysPro Asn Ser Ser Ile Val Tyr Glu Ala Asp Asp Leu Ile Leu His 85 90 95 AlaPro Gly Cys Val Pro Cys Val Arg Lys Asp Asn Val Ser Arg Cys 100 105 110Trp Val Gln Ile Thr Pro Thr Leu Ser Ala Pro Ser Phe Gly Ala Val 115 120125 Thr Ala Pro Leu Arg Arg Ala Val Asp Tyr Leu Val Gly Gly Ala Ala 130135 140 Leu Cys Ser Ala Leu Tyr Val Gly Asp Ala Cys Gly Ala Leu Phe Leu145 150 155 160 Val Gly Gln Met Phe Thr Tyr Arg Pro Arg Gln His Ala ThrVal Gln 165 170 175 Asp Cys Asn Cys Ser Ile Tyr Ser Gly His Val Thr GlyHis Gln Met 180 185 190 Ala 197 1485 DNA hepatitis C virus misc_feature(787)..(787) “n” is any nucleotide 197 tgtgccagga ccatcaccac cggagcttctatcacatact ccacttacgg caagttcctt 60 gctgatggag ggtgttcagg cggcgcgcatgacgtgatca tatgcgacga gtgccattcc 120 caggacgcca ccaccattct tgggataggcactgtccttg accaggcaga gacggctgga 180 gctaggctcg tcgtcttggc cacggccacccctcccggca gtgtgacaac gccccacccc 240 aacatcgagg aagtggccct gcctcaggagggggaggttc ccttctacgg cagagccatt 300 ccccttgctt ttataaaggg tggtaggcatctcatcttct gccattccaa gaaaaaatgt 360 gatgaactcg ccaagcaact gaccagcctgggcgtgaacg ccgtggcata ttatagaggt 420 ctagacgtcg ccgtcatacc cacaacaggagacgtggtcg tgtgcagcac cgacgcgctc 480 atgacgggat tcaccggcga ctttgattctgtcatagact gcaactccgc cgtcactcag 540 acggtggact tcagtctgga tcccacttttaccattgaga ctaccacagt gccccaggac 600 gcagtgtcca gaagccagcg ttggggccgcacggggagag gtaggcacgg catataccgg 660 tatgtctcgg ctggagagag accgtctggcatgttcgact ccgtggtgct ctgtgagtgc 720 tacgatgccg gatgtgcatg gtacgatctgactcctgccg agactaccgt gaggttgcgc 780 gcttacntaa acacccccgg gctccctgtctgtcaggacc atttggaatt ctgggagggg 840 gtgttcacgg ggctcactaa catcgacgctcacatgctgt cacagaccaa acagggtggg 900 gagaatttcc cataccttgt agcgtaccaagcaacagtct gtgttcgcgc gaaagcgccc 960 ccccccagct gggacacaat gtggaaatgcatgctccgtc tcaaaccgac nttaactggc 1020 cctactcccc tcttgtacag gctggggcccgtccagaatg agatcacact gacgcacccc 1080 atcaccaagt acattatggc ttgcatgtctgcggacttgg aggtcattac cagcacttgg 1140 gttctggtgg ggggcgttgt ggcggccctggcggcctact gcttgacggt gggttcggta 1200 gccatagtcg gtaggatcat cctctctgggaaacctgcca tcattcccga tagggaggta 1260 ttataccagc aatttgatga gatggaggagtgctcggcct cgttgcccta tatggacgaa 1320 acacgtgcca ttgccggaca attcaaagagaaagtgctcg gcttcatcag cacgaccggc 1380 cagaaggctg aaactctgaa gccggcagccacgtctgtgt ggaacaaggc tgagcagttc 1440 tggnccacat acatgtggaa cttcatcagtgggatacaat aatag 1485 198 484 PRT hepatitis C virus MISC_FEATURE(263)..(263) “Xaa” is any amino acid 198 Cys Ala Arg Thr Ile Thr Thr GlyAla Ser Ile Thr Tyr Ser Thr Tyr 1 5 10 15 Gly Lys Phe Leu Ala Asp GlyGly Cys Ser Gly Gly Ala His Asp Val 20 25 30 Ile Ile Cys Asp Glu Cys HisSer Gln Asp Ala Thr Thr Ile Leu Gly 35 40 45 Ile Gly Thr Val Leu Asp GlnAla Glu Thr Ala Gly Ala Arg Leu Val 50 55 60 Val Leu Ala Thr Ala Thr ProPro Gly Ser Val Thr Thr Pro His Pro 65 70 75 80 Asn Ile Glu Glu Val AlaLeu Pro Gln Glu Gly Glu Val Pro Phe Tyr 85 90 95 Gly Arg Ala Ile Pro LeuAla Phe Ile Lys Gly Gly Arg His Leu Ile 100 105 110 Phe Cys His Ser LysLys Lys Cys Asp Glu Leu Ala Lys Gln Leu Thr 115 120 125 Ser Leu Gly ValAsn Ala Val Ala Tyr Tyr Arg Gly Leu Asp Val Ala 130 135 140 Val Ile ProThr Thr Gly Asp Val Val Val Cys Ser Thr Asp Ala Leu 145 150 155 160 MetThr Gly Phe Thr Gly Asp Phe Asp Ser Val Ile Asp Cys Asn Ser 165 170 175Ala Val Thr Gln Thr Val Asp Phe Ser Leu Asp Pro Thr Phe Thr Ile 180 185190 Glu Thr Thr Thr Val Pro Gln Asp Ala Val Ser Arg Ser Gln Arg Trp 195200 205 Gly Arg Thr Gly Arg Gly Arg His Gly Ile Tyr Arg Tyr Val Ser Ala210 215 220 Gly Glu Arg Pro Ser Gly Met Phe Asp Ser Val Val Leu Cys GluCys 225 230 235 240 Tyr Asp Ala Gly Cys Ala Trp Tyr Asp Leu Thr Pro AlaGlu Thr Thr 245 250 255 Val Arg Leu Arg Ala Tyr Xaa Asn Thr Pro Gly LeuPro Val Cys Gln 260 265 270 Asp His Leu Glu Phe Trp Glu Gly Val Phe ThrGly Leu Thr Asn Ile 275 280 285 Asp Ala His Met Leu Ser Gln Thr Lys GlnGly Gly Glu Asn Phe Pro 290 295 300 Tyr Leu Val Ala Tyr Gln Ala Thr ValCys Val Arg Ala Lys Ala Pro 305 310 315 320 Pro Pro Ser Trp Asp Thr MetTrp Lys Cys Met Leu Arg Leu Lys Pro 325 330 335 Xaa Leu Thr Gly Pro ThrPro Leu Leu Tyr Arg Leu Gly Pro Val Gln 340 345 350 Asn Glu Ile Thr LeuThr His Pro Ile Thr Lys Tyr Ile Met Ala Cys 355 360 365 Met Ser Ala AspLeu Glu Val Ile Thr Ser Thr Trp Val Leu Val Gly 370 375 380 Gly Val ValAla Ala Leu Ala Ala Tyr Cys Leu Thr Val Gly Ser Val 385 390 395 400 AlaIle Val Gly Arg Ile Ile Leu Ser Gly Lys Pro Ala Ile Ile Pro 405 410 415Asp Arg Glu Val Leu Tyr Gln Gln Phe Asp Glu Met Glu Glu Cys Ser 420 425430 Ala Ser Leu Pro Tyr Met Asp Glu Thr Arg Ala Ile Ala Gly Gln Phe 435440 445 Lys Glu Lys Val Leu Gly Phe Ile Ser Thr Thr Gly Gln Lys Ala Glu450 455 460 Thr Leu Lys Pro Ala Ala Thr Ser Val Trp Asn Lys Ala Glu GlnPhe 465 470 475 480 Trp Xaa Thr Tyr 199 1485 DNA hepatitis C virusmisc_feature (684)..(684) “n” is any nucleotide 199 tgtgccaggaccatcaccac cggagcttct atcacatact ccacttacgg caagttcctt 60 gctgatggagggtgttcagg cggcgcgtat gacgtgatca tatgcgacga gtgccattcc 120 caggacgccaccaccattct tgggataggc actgtccttg accaggcaga gacggctgga 180 gctaggctcgtcgtcttggc cacggccacc cctcccggca gtgtgacaac gccccacccc 240 aacatcgaggaagtggccct gcctcaggag ggggaggttc ccttctacgg cagagccatt 300 ccccttgcttttataaaggg tggtaggcat ctcatcttct gccattccaa gaaaaaatgt 360 gatgaactcgccaagcaact gaccagcctg ggcgtgaacg ccgtggcata ttatagaggt 420 ctagacgtcgccgtcatccc cacagcagga gacgtggtcg tgtgcagcac cgacgcgctc 480 atgacgggattcaccggcga ctttgattct gtcatagact gcaactccgc cgtcactcag 540 acggtggacttcagtctgga tcccactttt accattgaga ctaccacagt gccccaggac 600 gcagtgtccagaagccagcg taggggccgc acggggagag gtaggcacgg catataccgg 660 tatgtctcggctggagagag accntctgac atgttcgact ccgtggtgct ctgtgagtgc 720 tacgatgccggatgtgcgtg gtatgatctg actcctgccg agactaccgt gaggttgcgc 780 gcttacataaacacccccgg gctccctgtc tgtcaggacc atttggaatt ctgggagggg 840 gtgttcacggggctcactaa catcgacgct cacatgctgt cacagaccaa acagggtggg 900 gagaatttnccataccttgt agcgtaccaa gcaacagtct gtgttcgcgc gaaagcgccc 960 ccccccagctgggacacaat gtggaaatgc atgctccgtc tcaaaccgac tttaactggc 1020 cctactcccctcttgtacag gctggggccc gtccagantg agatcacact gacgcacccc 1080 atcaccaagtacattatggc ttgcatgtct gcggacttgg aggtcattac cancacttgg 1140 gttctggtggggggcgttgt ggcggccctg gcggcctact gcttgacggt gggttcggta 1200 gccatagtcggtaggatcat cctctctggg aaacctgcca tcattcccga tagggaggca 1260 ttataccagcaatttgatga gatggaggag tgctcggcct cgttgcccta tatggacgag 1320 acacgtgccattgccggaca attcaaagag aaagtgctcg gcttcatcag cacgaccggc 1380 cagaaggctgaaactctgaa gccggcagcc acgtctgtgt ggaacaaggc tgagcagttc 1440 tgggccacatacatgtggaa cttcatcagc gggatacaat aatag 1485 200 484 PRT hepatitis Cvirus MISC_FEATURE (228)..(228) “Xaa” is any amino acid 200 Cys Ala ArgThr Ile Thr Thr Gly Ala Ser Ile Thr Tyr Ser Thr Tyr 1 5 10 15 Gly LysPhe Leu Ala Asp Gly Gly Cys Ser Gly Gly Ala Tyr Asp Val 20 25 30 Ile IleCys Asp Glu Cys His Ser Gln Asp Ala Thr Thr Ile Leu Gly 35 40 45 Ile GlyThr Val Leu Asp Gln Ala Glu Thr Ala Gly Ala Arg Leu Val 50 55 60 Val LeuAla Thr Ala Thr Pro Pro Gly Ser Val Thr Thr Pro His Pro 65 70 75 80 AsnIle Glu Glu Val Ala Leu Pro Gln Glu Gly Glu Val Pro Phe Tyr 85 90 95 GlyArg Ala Ile Pro Leu Ala Phe Ile Lys Gly Gly Arg His Leu Ile 100 105 110Phe Cys His Ser Lys Lys Lys Cys Asp Glu Leu Ala Lys Gln Leu Thr 115 120125 Ser Leu Gly Val Asn Ala Val Ala Tyr Tyr Arg Gly Leu Asp Val Ala 130135 140 Val Ile Pro Thr Ala Gly Asp Val Val Val Cys Ser Thr Asp Ala Leu145 150 155 160 Met Thr Gly Phe Thr Gly Asp Phe Asp Ser Val Ile Asp CysAsn Ser 165 170 175 Ala Val Thr Gln Thr Val Asp Phe Ser Leu Asp Pro ThrPhe Thr Ile 180 185 190 Glu Thr Thr Thr Val Pro Gln Asp Ala Val Ser ArgSer Gln Arg Arg 195 200 205 Gly Arg Thr Gly Arg Gly Arg His Gly Ile TyrArg Tyr Val Ser Ala 210 215 220 Gly Glu Arg Xaa Ser Asp Met Phe Asp SerVal Val Leu Cys Glu Cys 225 230 235 240 Tyr Asp Ala Gly Cys Ala Trp TyrAsp Leu Thr Pro Ala Glu Thr Thr 245 250 255 Val Arg Leu Arg Ala Tyr IleAsn Thr Pro Gly Leu Pro Val Cys Gln 260 265 270 Asp His Leu Glu Phe TrpGlu Gly Val Phe Thr Gly Leu Thr Asn Ile 275 280 285 Asp Ala His Met LeuSer Gln Thr Lys Gln Gly Gly Glu Asn Xaa Pro 290 295 300 Tyr Leu Val AlaTyr Gln Ala Thr Val Cys Val Arg Ala Lys Ala Pro 305 310 315 320 Pro ProSer Trp Asp Thr Met Trp Lys Cys Met Leu Arg Leu Lys Pro 325 330 335 ThrLeu Thr Gly Pro Thr Pro Leu Leu Tyr Arg Leu Gly Pro Val Gln 340 345 350Xaa Glu Ile Thr Leu Thr His Pro Ile Thr Lys Tyr Ile Met Ala Cys 355 360365 Met Ser Ala Asp Leu Glu Val Ile Thr Xaa Thr Trp Val Leu Val Gly 370375 380 Gly Val Val Ala Ala Leu Ala Ala Tyr Cys Leu Thr Val Gly Ser Val385 390 395 400 Ala Ile Val Gly Arg Ile Ile Leu Ser Gly Lys Pro Ala IleIle Pro 405 410 415 Asp Arg Glu Ala Leu Tyr Gln Gln Phe Asp Glu Met GluGlu Cys Ser 420 425 430 Ala Ser Leu Pro Tyr Met Asp Glu Thr Arg Ala IleAla Gly Gln Phe 435 440 445 Lys Glu Lys Val Leu Gly Phe Ile Ser Thr ThrGly Gln Lys Ala Glu 450 455 460 Thr Leu Lys Pro Ala Ala Thr Ser Val TrpAsn Lys Ala Glu Gln Phe 465 470 475 480 Trp Ala Thr Tyr 201 340 DNAhepatitis C virus 201 ctccactgtg actgagagag acatcagggt cgaagaagaagtctatcagt gttgtgatct 60 ggagcccgag gcccgcaagg taataaccgc cctcacggagagactctacg tgggcggccc 120 tatgtacaat agcaagggag acctttgcgg gtatcgcaggtgccgcgcaa gcggcgtata 180 taccaccagc ttcgggaaca cactgacgtg ctaccttaaagcctcagcag ccatcagggc 240 tgcggggctg aaggactgca ccatgctggt ttgcggtgacgacttagtcg tgatcgctga 300 aagcggtggc gtcgaggagg acaagcgagc cctcggagct340 202 113 PRT hepatitis C virus 202 Ser Thr Val Thr Glu Arg Asp IleArg Val Glu Glu Glu Val Tyr Gln 1 5 10 15 Cys Cys Asp Leu Glu Pro GluAla Arg Lys Val Ile Thr Ala Leu Thr 20 25 30 Glu Arg Leu Tyr Val Gly GlyPro Met Tyr Asn Ser Lys Gly Asp Leu 35 40 45 Cys Gly Tyr Arg Arg Cys ArgAla Ser Gly Val Tyr Thr Thr Ser Phe 50 55 60 Gly Asn Thr Leu Thr Cys TyrLeu Lys Ala Ser Ala Ala Ile Arg Ala 65 70 75 80 Ala Gly Leu Lys Asp CysThr Met Leu Val Cys Gly Asp Asp Leu Val 85 90 95 Val Ile Ala Glu Ser GlyGly Val Glu Glu Asp Lys Arg Ala Leu Gly 100 105 110 Ala 203 340 DNAhepatitis C virus 203 ctccacagtg actgaaagag acatcagggt cgaggaagaggtctaccagt gttgtgacct 60 ggagcctgaa acccgcaagg taatatctgc cctcactgaaagactctatg tgggcggtcc 120 catgcacaac agcaggggag acctatgcgg gtaccgtagatgccgcgcga gcggcgtata 180 caccacaagc ttcgggaaca ctctgacgtg cttcctcaaggccacagcgg ccaccaaagc 240 cgctggccta aaggactgca ccatgttggt gtgtggtgacgacttagtcg ttatcgccga 300 aagcgatggt gtcgaagagg accgccgagc cctcggagct340 204 113 PRT hepatitis C virus 204 Ser Thr Val Thr Glu Arg Asp IleArg Val Glu Glu Glu Val Tyr Gln 1 5 10 15 Cys Cys Asp Leu Glu Pro GluThr Arg Lys Val Ile Ser Ala Leu Thr 20 25 30 Glu Arg Leu Tyr Val Gly GlyPro Met His Asn Ser Arg Gly Asp Leu 35 40 45 Cys Gly Tyr Arg Arg Cys ArgAla Ser Gly Val Tyr Thr Thr Ser Phe 50 55 60 Gly Asn Thr Leu Thr Cys PheLeu Lys Ala Thr Ala Ala Thr Lys Ala 65 70 75 80 Ala Gly Leu Lys Asp CysThr Met Leu Val Cys Gly Asp Asp Leu Val 85 90 95 Val Ile Ala Glu Ser AspGly Val Glu Glu Asp Arg Arg Ala Leu Gly 100 105 110 Ala 205 340 DNAhepatitis C virus 205 ctccacggtg accgaaaggg atatcaggac cgaggaagagatctaccagt gctgcgacct 60 ggagcccgaa gcccgcaagg tgatatccgc cctaacggaaagactctacg tgggcggtcc 120 catgtacaac tccaaggggg acctatgcgg gcaacggaggtgccgcgcaa gcggggtcta 180 caccaccagc ttcgggaaca ctgtaacgtg ttatctcaaggccgttgcgg ctactagggc 240 cgcaggtctg aaaggttgca gcatgctggt ttgtggagacgacttagtcg tcatctgcga 300 gagcggcggc gtagaggagg atgcaagagc cctccgagcc340 206 113 PRT hepatitis C virus 206 Ser Thr Val Thr Glu Arg Asp IleArg Thr Glu Glu Glu Ile Tyr Gln 1 5 10 15 Cys Cys Asp Leu Glu Pro GluAla Arg Lys Val Ile Ser Ala Leu Thr 20 25 30 Glu Arg Leu Tyr Val Gly GlyPro Met Tyr Asn Ser Lys Gly Asp Leu 35 40 45 Cys Gly Gln Arg Arg Cys ArgAla Ser Gly Val Tyr Thr Thr Ser Phe 50 55 60 Gly Asn Thr Val Thr Cys TyrLeu Lys Ala Val Ala Ala Thr Arg Ala 65 70 75 80 Ala Gly Leu Lys Gly CysSer Met Leu Val Cys Gly Asp Asp Leu Val 85 90 95 Val Ile Cys Glu Ser GlyGly Val Glu Glu Asp Ala Arg Ala Leu Arg 100 105 110 Ala 207 340 DNAhepatitis C virus 207 ctccacggtg actgaaaggg acattagggt cgaggaagagatctaccagt gctgtgacct 60 ggagcccgag gcacgcaagg tgatatccgc tctcacagaaagactctaca agggcggccc 120 catgtataac agcaaggggg acctatgcgg gcttcggaggtgccgcgcaa gcggggtata 180 caccacaagc ttcgggaaca cggtgacatg ctaccttaaagccacagcag ccaccagggc 240 tgcagggctg aaagattgca ctatgctggt atgcggtgacgacttagtcg ttattgccga 300 aagcggtggc gtggaggagg acgcccgagc cctccgagcc340 208 113 PRT hepatitis C virus 208 Ser Thr Val Thr Glu Arg Asp IleArg Val Glu Glu Glu Ile Tyr Gln 1 5 10 15 Cys Cys Asp Leu Glu Pro GluAla Arg Lys Val Ile Ser Ala Leu Thr 20 25 30 Glu Arg Leu Tyr Lys Gly GlyPro Met Tyr Asn Ser Lys Gly Asp Leu 35 40 45 Cys Gly Leu Arg Arg Cys ArgAla Ser Gly Val Tyr Thr Thr Ser Phe 50 55 60 Gly Asn Thr Val Thr Cys TyrLeu Lys Ala Thr Ala Ala Thr Arg Ala 65 70 75 80 Ala Gly Leu Lys Asp CysThr Met Leu Val Cys Gly Asp Asp Leu Val 85 90 95 Val Ile Ala Glu Ser GlyGly Val Glu Glu Asp Ala Arg Ala Leu Arg 100 105 110 Ala 209 340 DNAhepatitis C virus misc_feature (13)..(13) “n” is any nucleotide 209ccccaccgtg acngagaggg acntcagggt cgaggaagag gtctatcagt gctgtaatct 60ggagnccgat gnccgcaagg tcatcaacgc cctcacagag agactctacg tgggcggccc 120tatgcacaac agcaagggag acctgtgtgg catccgtaga tgccgcgcga gcggcgttta 180caccacgagc ttcggaaaca cgctgacttg ctacctcaaa gccacagcgg ccaccagggc 240cgcgggcttg aaggattgca ccatgctggt ctgcggngac gacctggttg tcattgctga 300gagcattggc atagacgagg acaagcaagc cctccgnact 340 210 113 PRT hepatitis Cvirus MISC_FEATURE (8)..(8) “Xaa” is any amino acid 210 Pro Thr Val ThrGlu Arg Asp Xaa Arg Val Glu Glu Glu Val Tyr Gln 1 5 10 15 Cys Cys AsnLeu Glu Xaa Asp Xaa Arg Lys Val Ile Asn Ala Leu Thr 20 25 30 Glu Arg LeuTyr Val Gly Gly Pro Met His Asn Ser Lys Gly Asp Leu 35 40 45 Cys Gly IleArg Arg Cys Arg Ala Ser Gly Val Tyr Thr Thr Ser Phe 50 55 60 Gly Asn ThrLeu Thr Cys Tyr Leu Lys Ala Thr Ala Ala Thr Arg Ala 65 70 75 80 Ala GlyLeu Lys Asp Cys Thr Met Leu Val Cys Gly Asp Asp Leu Val 85 90 95 Val IleAla Glu Ser Ile Gly Ile Asp Glu Asp Lys Gln Ala Leu Arg 100 105 110 Thr211 340 DNA hepatitis C virus misc_feature (11)..(11) “n” is anynucleotide 211 ctcgactgtg nccgagaggg acatcaggac agagggagag gtctatcagtgttgcgacct 60 ggaaccggaa gcccgcaagg taatcaccgc cctcactgag agactctatgtgggcggacc 120 catgttcaac agcaagggag acctgtgcgg acaacgccgg tgccgcgcaagcggcgtgtt 180 caccaccagc ttcgggaaca cactgacgtg ctaccttaaa gccacagctgctactagagc 240 agccggctta aaagattgca ccatgctggt ctgcggtgac gacttagtcgttatttccga 300 gagcgccggt gtggaggagg atcccanaac ccnncgaccn 340 212 113PRT hepatitis C virus MISC_FEATURE (4)..(4) “Xaa” is any amino acid 212Ser Thr Val Xaa Glu Arg Asp Ile Arg Thr Glu Gly Glu Val Tyr Gln 1 5 1015 Cys Cys Asp Leu Glu Pro Glu Ala Arg Lys Val Ile Thr Ala Leu Thr 20 2530 Glu Arg Leu Tyr Val Gly Gly Pro Met Phe Asn Ser Lys Gly Asp Leu 35 4045 Cys Gly Gln Arg Arg Cys Arg Ala Ser Gly Val Phe Thr Thr Ser Phe 50 5560 Gly Asn Thr Leu Thr Cys Tyr Leu Lys Ala Thr Ala Ala Thr Arg Ala 65 7075 80 Ala Gly Leu Lys Asp Cys Thr Met Leu Val Cys Gly Asp Asp Leu Val 8590 95 Val Ile Ser Glu Ser Ala Gly Val Glu Glu Asp Pro Xaa Thr Xaa Arg100 105 110 Pro 213 340 DNA hepatitis C virus 213 ctcaacagtc accgagaacgacatccgtgt tgaggagtca atttaccaat gttgtgactt 60 ggcccccgag gccagacaggccataaagtc gctcacagag cggctttata tcgggggtcc 120 cctgactaat tcaaaggggcagaactgtgg ctatcgccga tgccgcgcaa gcggcgtgct 180 gacgaccagc tgcggtaatacccttacatg ttacctaaag gcctctgcag cctgtcgagc 240 tgcgaagctc caggactgcacgatgctcgt gtgcggggac gaccttgtcg ttatctgtga 300 aagcgcggga acccaagaggacgcggcgag cctacgagtc 340 214 113 PRT hepatitis C virus 214 Ser Thr ValThr Glu Asn Asp Ile Arg Val Glu Glu Ser Ile Tyr Gln 1 5 10 15 Cys CysAsp Leu Ala Pro Glu Ala Arg Gln Ala Ile Lys Ser Leu Thr 20 25 30 Glu ArgLeu Tyr Ile Gly Gly Pro Leu Thr Asn Ser Lys Gly Gln Asn 35 40 45 Cys GlyTyr Arg Arg Cys Arg Ala Ser Gly Val Leu Thr Thr Ser Cys 50 55 60 Gly AsnThr Leu Thr Cys Tyr Leu Lys Ala Ser Ala Ala Cys Arg Ala 65 70 75 80 AlaLys Leu Gln Asp Cys Thr Met Leu Val Cys Gly Asp Asp Leu Val 85 90 95 ValIle Cys Glu Ser Ala Gly Thr Gln Glu Asp Ala Ala Ser Leu Arg 100 105 110Val 215 340 DNA hepatitis C virus 215 ctcaaccgtc acggagaggg atataagaacagaagaatcc atatatcaag cttgttccct 60 gccccaagag gccagaactg tcatacactcgctcaccgag agactctacg tgggagggcc 120 catgataaac agcaaagggc aatcctgcggttacaggcgt tgccgcgcaa gcggtgtttt 180 caccaccagc atggggaata ccatgacgtgttacatcaaa gcccttgcag cgtgtaaagc 240 cgcagggatc gtggaccccg tcatgctggtgtgtggagac gacctggtcg tcatctcgga 300 gagccagggt aacgaggagg acgagcgaaacctgagagct 340 216 113 PRT hepatitis C virus 216 Ser Thr Val Thr Glu ArgAsp Ile Arg Thr Glu Glu Ser Ile Tyr Gln 1 5 10 15 Ala Cys Ser Leu ProGln Glu Ala Arg Thr Val Ile His Ser Leu Thr 20 25 30 Glu Arg Leu Tyr ValGly Gly Pro Met Ile Asn Ser Lys Gly Gln Ser 35 40 45 Cys Gly Tyr Arg ArgCys Arg Ala Ser Gly Val Phe Thr Thr Ser Met 50 55 60 Gly Asn Thr Met ThrCys Tyr Ile Lys Ala Leu Ala Ala Cys Lys Ala 65 70 75 80 Ala Gly Ile ValAsp Pro Val Met Leu Val Cys Gly Asp Asp Leu Val 85 90 95 Val Ile Ser GluSer Gln Gly Asn Glu Glu Asp Glu Arg Asn Leu Arg 100 105 110 Ala 217 340DNA hepatitis C virus 217 ctcgactgtc actgaacagg acatcagggt ggaagaggagatatatcaat gctgcaacct 60 tgaaccggag gccaggaaag tgatctcctc cctcacggagcggctttact gcggaggccc 120 tatgtttaac agcaaggggg cccagtgtgg ttatcgccgttgccgtgcca gtggagttct 180 gcctaccagc tttggcaaca caatcacttg ttacatcaaggccacaacgg ccgcgaaggc 240 cgcaggcctc cggaacccgg actttcttgt ctgcggagatgatctggtcg tggtggctga 300 gagtgatggc gtcgacgagg atagagcagc cctgagagcc340 218 113 PRT hepatitis C virus 218 Ser Thr Val Thr Glu Gln Asp IleArg Val Glu Glu Glu Ile Tyr Gln 1 5 10 15 Cys Cys Asn Leu Glu Pro GluAla Arg Lys Val Ile Ser Ser Leu Thr 20 25 30 Glu Arg Leu Tyr Cys Gly GlyPro Met Phe Asn Ser Lys Gly Ala Gln 35 40 45 Cys Gly Tyr Arg Arg Cys ArgAla Ser Gly Val Leu Pro Thr Ser Phe 50 55 60 Gly Asn Thr Ile Thr Cys TyrIle Lys Ala Thr Thr Ala Ala Lys Ala 65 70 75 80 Ala Gly Leu Arg Asn ProAsp Phe Leu Val Cys Gly Asp Asp Leu Val 85 90 95 Val Val Ala Glu Ser AspGly Val Asp Glu Asp Arg Ala Ala Leu Arg 100 105 110 Ala 219 10 PRThepatitis C virus 219 Arg Ser Glu Gly Arg Thr Ser Trp Ala Gln 1 5 10 22010 PRT hepatitis C virus 220 Arg Ser Glu Gly Arg Thr Ser Trp Ala Gln 1 510 221 10 PRT hepatitis C virus 221 Arg Thr Glu Gly Arg Thr Ser Trp AlaGln 1 5 10 222 629 DNA hepatitis C virus 222 tagacttttg ggagagcgtcttcactggac taactcacat agatgcccac tttctgtcac 60 agactaagca gcagggactcaacttctcgt tcctgactgc ctaccaagcc actgtgtgcg 120 ctcgcgcgca ggctcctcccccaagttggg acgagatgtg gaagtgtctc gtacggctta 180 agccaacact acatggacctacgcctcttc tatatcggtt ggggcctgtc caaaatgaaa 240 tctgcttgac acaccccatcacaaaataca tcatggcatg catgtcagct gatctggaag 300 taaccaccag cacctgggttttgcttggag gggtcctcgc ggccctagcg gcctactgct 360 tgtcagtcgg ttgtgttgtgattgtgggtc atatcgagct ggggggcaag ccggcaatcg 420 ttccagacaa agaggtgttgtatcaacaat acgatgagat ggaagagtgc tcacaagctg 480 ccccatatat cgaacaagctcaggtaatag ctcaccagtt caaggaaaaa gtccttggat 540 tgctgcagcg agccacccaacaacaagctg tcattgagcc catagtaact accaactggc 600 aaaagcttga ggccttttggcacaagcat 629 223 209 PRT hepatitis C virus 223 Asp Phe Trp Glu Ser ValPhe Thr Gly Leu Thr His Ile Asp Ala His 1 5 10 15 Phe Leu Ser Gln ThrLys Gln Gln Gly Leu Asn Phe Ser Phe Leu Thr 20 25 30 Ala Tyr Gln Ala ThrVal Cys Ala Arg Ala Gln Ala Pro Pro Pro Ser 35 40 45 Trp Asp Glu Met TrpLys Cys Leu Val Arg Leu Lys Pro Thr Leu His 50 55 60 Gly Pro Thr Pro LeuLeu Tyr Arg Leu Gly Pro Val Gln Asn Glu Ile 65 70 75 80 Cys Leu Thr HisPro Ile Thr Lys Tyr Ile Met Ala Cys Met Ser Ala 85 90 95 Asp Leu Glu ValThr Thr Ser Thr Trp Val Leu Leu Gly Gly Val Leu 100 105 110 Ala Ala LeuAla Ala Tyr Cys Leu Ser Val Gly Cys Val Val Ile Val 115 120 125 Gly HisIle Glu Leu Gly Gly Lys Pro Ala Ile Val Pro Asp Lys Glu 130 135 140 ValLeu Tyr Gln Gln Tyr Asp Glu Met Glu Glu Cys Ser Gln Ala Ala 145 150 155160 Pro Tyr Ile Glu Gln Ala Gln Val Ile Ala His Gln Phe Lys Glu Lys 165170 175 Val Leu Gly Leu Leu Gln Arg Ala Thr Gln Gln Gln Ala Val Ile Glu180 185 190 Pro Ile Val Thr Thr Asn Trp Gln Lys Leu Glu Ala Phe Trp HisLys 195 200 205 His 224 12 PRT hepatitis C virus 224 Ile His Tyr Arg AsnAla Ser Gly Ile Tyr His Ile 1 5 10 225 12 PRT hepatitis C virus 225 ValAsn Tyr Arg Asn Ala Ser Gly Ile Tyr His Ile 1 5 10 226 12 PRT hepatitisC virus 226 Val Asn Tyr Arg Asn Ala Ser Gly Val Tyr His Ile 1 5 10 22712 PRT hepatitis C virus 227 Val Asn Tyr His Asn Thr Ser Gly Ile Tyr HisLeu 1 5 10 228 12 PRT hepatitis C virus 228 Gln His Tyr Arg Asn Ala SerGly Ile Tyr His Val 1 5 10 229 12 PRT hepatitis C virus 229 Gln His TyrArg Asn Val Ser Gly Ile Tyr His Val 1 5 10 230 12 PRT hepatitis C virus230 Ile His Tyr Arg Asn Ala Ser Asp Gly Tyr Tyr Ile 1 5 10 231 12 PRThepatitis C virus 231 Leu Gln Val Lys Asn Thr Ser Ser Ser Tyr Met Val 15 10 232 11 PRT hepatitis C virus 232 Val Trp Gln Leu Arg Ala Ile ValLeu His Val 1 5 10 233 11 PRT hepatitis C virus 233 Val Tyr Glu Ala AspTyr His Ile Leu His Leu 1 5 10 234 11 PRT hepatitis C virus 234 Val TyrGlu Thr Asp Asn His Ile Leu His Leu 1 5 10 235 11 PRT hepatitis C virus235 Val Tyr Glu Thr Glu Asn His Ile Leu His Leu 1 5 10 236 11 PRThepatitis C virus 236 Val Phe Glu Thr Val His His Ile Leu His Leu 1 5 10237 11 PRT hepatitis C virus 237 Val Phe Glu Thr Glu His His Ile Leu HisLeu 1 5 10 238 11 PRT hepatitis C virus 238 Val Phe Glu Thr Asp His HisIle Met His Leu 1 5 10 239 11 PRT hepatitis C virus 239 Val Tyr Glu ThrGlu Asn His Ile Leu His Leu 1 5 10 240 11 PRT hepatitis C virus 240 ValTyr Glu Ala Asp Ala Leu Ile Leu His Ala 1 5 10 241 13 PRT hepatitis Cvirus 241 Val Gln Asp Gly Asn Thr Ser Ala Cys Trp Thr Pro Val 1 5 10 24213 PRT hepatitis C virus 242 Val Lys Thr Gly Asn Gln Ser Arg Cys Trp ValAla Leu 1 5 10 243 13 PRT hepatitis C virus 243 Val Lys Thr Gly Asn GlnSer Arg Cys Trp Val Ala Leu 1 5 10 244 13 PRT hepatitis C virus 244 ValArg Thr Gly Asn Gln Ser Arg Cys Trp Val Ala Leu 1 5 10 245 13 PRThepatitis C virus 245 Val Lys Thr Gly Asn Gln Ser Arg Cys Trp Ile AlaLeu 1 5 10 246 13 PRT hepatitis C virus 246 Val Lys Thr Gly Asn Gln SerArg Cys Trp Ile Ala Leu 1 5 10 247 13 PRT hepatitis C virus 247 Val LysThr Gly Asn Ser Val Arg Cys Trp Ile Pro Leu 1 5 10 248 13 PRT hepatitisC virus 248 Val Lys Thr Gly Asn Val Ser Arg Cys Trp Ile Ser Leu 1 5 10249 13 PRT hepatitis C virus 249 Val Arg Lys Asp Asn Val Ser Arg Cys TrpVal Gln Ile 1 5 10 250 10 PRT hepatitis C virus 250 Ala Pro Ser Phe GlyAla Val Thr Ala Pro 1 5 10 251 10 PRT hepatitis C virus 251 Val Ser GlnPro Gly Ala Leu Thr Lys Gly 1 5 10 252 10 PRT hepatitis C virus 252 ValLys Tyr Val Gly Ala Thr Thr Ala Ser 1 5 10 253 10 PRT hepatitis C virus253 Ala Pro Tyr Ile Gly Ala Pro Val Glu Ser 1 5 10 254 10 PRT hepatitisC virus 254 Ala Gln His Leu Asn Ala Pro Leu Glu Ser 1 5 10 255 10 PRThepatitis C virus 255 Ser Pro Tyr Val Gly Ala Pro Leu Glu Pro 1 5 10 25610 PRT hepatitis C virus 256 Ser Pro Tyr Ala Gly Ala Pro Leu Glu Pro 1 510 257 10 PRT hepatitis C virus 257 Ala Pro Tyr Leu Gly Ala Pro Leu GluSer 1 5 10 258 10 PRT hepatitis C virus 258 Ala Pro Tyr Leu Gly Ala ProLeu Glu Ser 1 5 10 259 10 PRT hepatitis C virus 259 Ala Pro Tyr Val GlyAla Pro Leu Glu Ser 1 5 10 260 11 PRT hepatitis C virus 260 Asn Val ProTyr Leu Gly Ala Pro Leu Thr Ser 1 5 10 261 10 PRT hepatitis C virus 261Ala Pro His Leu Arg Ala Pro Leu Ser Ser 1 5 10 262 10 PRT hepatitis Cvirus 262 Ala Pro Tyr Leu Gly Ala Pro Leu Thr Ser 1 5 10 263 10 PRThepatitis C virus 263 Arg Pro Arg Gln His Ala Thr Val Gln Asp 1 5 10 26410 PRT hepatitis C virus 264 Ser Pro Gln His His Lys Phe Val Gln Asp 1 510 265 10 PRT hepatitis C virus 265 Arg Pro Arg Arg Leu Trp Thr Thr GlnGlu 1 5 10 266 10 PRT hepatitis C virus 266 Pro Pro Arg Ile His Glu ThrThr Gln Asp 1 5 10 267 14 PRT hepatitis C virus 267 Thr Ile Ser Tyr AlaAsn Gly Ser Gly Pro Ser Asp Asp Lys 1 5 10 268 19 PRT hepatitis C virus268 Ser Arg Arg Gln Pro Ile Pro Arg Ala Arg Arg Thr Glu Gly Arg Ser 1 510 15 Trp Ala Gln 269 1443 DNA hepatitis C virus 269 accatcaccaccggagcttc tatcacatac tccacttacg gcaagttcct tgctgatgga 60 gggtgttcaggcggcgcgta tgacgtgatc atatgcgacg agtgccattc ccaggacgcc 120 accaccattcttgggatagg cactgtcctt gaccaggcag agacggctgg agctaggctc 180 gtcgtcttggccacggccac ccctcccggc agtgtgacaa cgccccaccc caacatcgag 240 gaagtggccctgcctcagga gggggaggtt cccttctacg gcagagccat tccccttgct 300 tttataaagggtggtaggca tctcatcttc tgccattcca agaaaaaatg tgatgaactc 360 gccaagcaactgaccagcct gggcgtgaac gccgtggcat attatagagg tctagacgtc 420 gccgtcatccccacagcagg agacgtggtc gtgtgcagca ccgacgcgct catgacggga 480 ttcaccggcgactttgattc tgtcatagac tgcaactccg ccgtcactca gacggtggac 540 ttcagtctggatcccacttt taccattgag actaccacag tgccccagga cgcagtgtcc 600 agaagccagcgtaggggccg cacggggaga ggtaggcacg gcatataccg gtatgtctcg 660 gctggagagagaccgtctga catgttcgac tccgtggtgc tctgtgagtg ctacgatgcc 720 ggatgtgcgtggtatgatct gactcctgcc gagactaccg tgaggttgcg cgcttacata 780 aacacccccgggctccctgt ctgtcaggac catttggaat tctgggaggg ggtgttcacg 840 gggctcactaacatcgacgc tcacatgctg tcacagacca aacagggtgg ggagaatttc 900 ccataccttgtagcgtacca agcaacagtc tgtgttcgcg cgaaagcgcc cccccccagc 960 tgggacacaatgtggaaatg catgctccgt ctcaaaccga ctttaactgg ccctactccc 1020 ctcttgtacaggctggggcc cgtccagaat gagatcacac tgacgcaccc catcaccaag 1080 tacattatggcttgcatgtc tgcggacttg gaggtcatta ccagcacttg ggttctggtg 1140 gggggcgttgtggcggccct ggcggcctac tgcttgacgg tgggttcggt agccatagtc 1200 ggtaggatcatcctctctgg gaaacctgcc atcattcccg atagggaggc attataccag 1260 caatttgatgagatggagga gtgctcggcc tcgttgccct atatggacga gacacgtgcc 1320 attgccggacaattcaaaga gaaagtgctc ggcttcatca gcacgaccgg ccagaaggct 1380 gaaactctgaagccggcagc cacgtctgtg tggaacaagg ctgagcagtt ctgggccaca 1440 tac 1443 270481 PRT hepatitis C virus 270 Thr Ile Thr Thr Gly Ala Ser Ile Thr TyrSer Thr Tyr Gly Lys Phe 1 5 10 15 Leu Ala Asp Gly Gly Cys Ser Gly GlyAla Tyr Asp Val Ile Ile Cys 20 25 30 Asp Glu Cys His Ser Gln Asp Ala ThrThr Ile Leu Gly Ile Gly Thr 35 40 45 Val Leu Asp Gln Ala Glu Thr Ala GlyAla Arg Leu Val Val Leu Ala 50 55 60 Thr Ala Thr Pro Pro Gly Ser Val ThrThr Pro His Pro Asn Ile Glu 65 70 75 80 Glu Val Ala Leu Pro Gln Glu GlyGlu Val Pro Phe Tyr Gly Arg Ala 85 90 95 Ile Pro Leu Ala Phe Ile Lys GlyGly Arg His Leu Ile Phe Cys His 100 105 110 Ser Lys Lys Lys Cys Asp GluLeu Ala Lys Gln Leu Thr Ser Leu Gly 115 120 125 Val Asn Ala Val Ala TyrTyr Arg Gly Leu Asp Val Ala Val Ile Pro 130 135 140 Thr Ala Gly Asp ValVal Val Cys Ser Thr Asp Ala Leu Met Thr Gly 145 150 155 160 Phe Thr GlyAsp Phe Asp Ser Val Ile Asp Cys Asn Ser Ala Val Thr 165 170 175 Gln ThrVal Asp Phe Ser Leu Asp Pro Thr Phe Thr Ile Glu Thr Thr 180 185 190 ThrVal Pro Gln Asp Ala Val Ser Arg Ser Gln Arg Arg Gly Arg Thr 195 200 205Gly Arg Gly Arg His Gly Ile Tyr Arg Tyr Val Ser Ala Gly Glu Arg 210 215220 Pro Ser Asp Met Phe Asp Ser Val Val Leu Cys Glu Cys Tyr Asp Ala 225230 235 240 Gly Cys Ala Trp Tyr Asp Leu Thr Pro Ala Glu Thr Thr Val ArgLeu 245 250 255 Arg Ala Tyr Ile Asn Thr Pro Gly Leu Pro Val Cys Gln AspHis Leu 260 265 270 Glu Phe Trp Glu Gly Val Phe Thr Gly Leu Thr Asn IleAsp Ala His 275 280 285 Met Leu Ser Gln Thr Lys Gln Gly Gly Glu Asn PhePro Tyr Leu Val 290 295 300 Ala Tyr Gln Ala Thr Val Cys Val Arg Ala LysAla Pro Pro Pro Ser 305 310 315 320 Trp Asp Thr Met Trp Lys Cys Met LeuArg Leu Lys Pro Thr Leu Thr 325 330 335 Gly Pro Thr Pro Leu Leu Tyr ArgLeu Gly Pro Val Gln Asn Glu Ile 340 345 350 Thr Leu Thr His Pro Ile ThrLys Tyr Ile Met Ala Cys Met Ser Ala 355 360 365 Asp Leu Glu Val Ile ThrSer Thr Trp Val Leu Val Gly Gly Val Val 370 375 380 Ala Ala Leu Ala AlaTyr Cys Leu Thr Val Gly Ser Val Ala Ile Val 385 390 395 400 Gly Arg IleIle Leu Ser Gly Lys Pro Ala Ile Ile Pro Asp Arg Glu 405 410 415 Ala LeuTyr Gln Gln Phe Asp Glu Met Glu Glu Cys Ser Ala Ser Leu 420 425 430 ProTyr Met Asp Glu Thr Arg Ala Ile Ala Gly Gln Phe Lys Glu Lys 435 440 445Val Leu Gly Phe Ile Ser Thr Thr Gly Gln Lys Ala Glu Thr Leu Lys 450 455460 Pro Ala Ala Thr Ser Val Trp Asn Lys Ala Glu Gln Phe Trp Ala Thr 465470 475 480 Tyr 271 5 PRT hepatitis C virus 271 Leu Glu Trp Arg Asn 1 5272 20 PRT hepatitis C virus 272 Leu Ser Gly Lys Pro Ala Ile Ile Pro AspArg Glu Val Leu Tyr Arg 1 5 10 15 Glu Phe Asp Glu 20 273 20 PRThepatitis C virus 273 Ser Gln His Leu Pro Tyr Ile Glu Gln Gly Met MetLeu Ala Glu Gln 1 5 10 15 Phe Lys Gln Lys 20 274 20 PRT hepatitis Cvirus 274 Leu Ala Glu Gln Phe Lys Gln Lys Ala Leu Gly Leu Leu Gln ThrAla 1 5 10 15 Ser Arg Gln Ala 20 275 20 PRT hepatitis C virus 275 LeuSer Gly Arg Pro Ala Val Ile Pro Asp Arg Glu Val Leu Tyr Gln 1 5 10 15Glu Phe Asp Glu 20 276 20 PRT hepatitis C virus 276 Ala Ser His Leu ProTyr Ile Glu Gln Gly Met Gln Leu Ala Glu Gln 1 5 10 15 Phe Lys Gln Lys 20277 20 PRT hepatitis C virus 277 Leu Ala Glu Gln Phe Lys Gln Lys Ala LeuGly Leu Leu Gln Thr Ala 1 5 10 15 Thr Lys Gln Ala 20 278 20 PRThepatitis C virus 278 Val Asn Gln Arg Ala Val Val Ala Pro Asp Lys GluVal Leu Tyr Glu 1 5 10 15 Ala Phe Asp Glu 20 279 20 PRT hepatitis Cvirus 279 Ala Ser Arg Ala Ala Leu Ile Glu Glu Gly Gln Arg Ile Ala GluMet 1 5 10 15 Leu Lys Ser Lys 20 280 20 PRT hepatitis C virus 280 IleAla Glu Met Leu Lys Ser Lys Ile Gln Gly Leu Leu Gln Gln Ala 1 5 10 15Ser Lys Gln Ala 20 281 20 PRT hepatitis C virus 281 Leu Asn Asp Arg ValVal Val Ala Pro Asp Lys Glu Ile Leu Tyr Glu 1 5 10 15 Ala Phe Asp Glu 20282 20 PRT hepatitis C virus 282 Ala Ser Lys Ala Ala Leu Ile Glu Glu GlyGln Arg Met Ala Glu Met 1 5 10 15 Leu Lys Ser Lys 20 283 20 PRThepatitis C virus 283 Met Ala Glu Met Leu Lys Ser Lys Ile Gln Gly LeuLeu Gln Gln Ala 1 5 10 15 Thr Arg Gln Ala 20 284 20 PRT hepatitis Cvirus 284 Ala Ala Ser Leu Pro Tyr Met Asp Glu Thr Arg Ala Ile Ala GlyGln 1 5 10 15 Phe Lys Glu Lys 20

What is claimed is:
 1. An isolated polynucleic acid sequence consistingof 8 or more contiguous nucleotides selected from: an HCV type 3agenomic sequence selected from the region spanning positions 417 to 957of the Core/E1 region of HCV subtype 3a, wherein said polynucleic acidsequence is capable of hybridizing to HCV subtype 3a, but not anothersubtype of HCV; the complement of said polynucleic acid, wherein saidpolynucleic acid contains at least one genotype 3a-specific nucleotide.2. A recombinant vector comprising a vector sequence; and a prokaryotic,eukaryotic or viral promoter sequence operably linked to a polynucleicacid sequence of claim
 1. 3. A kit for determining the presence of HCVgenotypes comprising a polynucleic acid sequence of claim
 1. 4. A methodof detecting or screening for one or more HCV genotypes present in abiological sample, comprising the following steps: (i) providing asample nucleic acid, (ii) determining the presence of a polynucleic acidsequence according to claim 1, by means of a sequencing reaction, and,(iii) inferring from the presence of one or more of these HCVpolynucleic acid sequences of step (ii) the genotype(s) present in saidsample.
 5. A method of detecting or screening for one or more HCVgenotypes present in a biological sample, comprising the followingsteps: (i) providing a sample nucleic acid, (ii) specifically amplifyinga polynucleic acid sequence according to claim 1, and, (iii) inferringfrom the presence of one or more amplified HCV polynucleic acidsequences of step (ii) the genotype(s) present in said sample.
 6. Anisolated HCV polynucleic acid according to claim 1, wherein saidpolynucleic acid is capable of acting as a primer for HCV type- orsubtype-specific amplification.
 7. An isolated HCV polynucleic acidaccording to claim 1, wherein said polynucleic acid is capable of actingas a probe for HCV type- or subtype-specific hybridisationhybridization.
 8. A method for detecting HCV nucleic acids present in abiological sample comprising the following steps: (i) providing a samplenucleic acid, (ii) determining the sequence of one or more HCVpolynucleic acids according to claim 1, present in said sample.